From 6e9fcb203616769db906f7d10c069fce043b4a9c Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Fri, 19 Sep 2025 16:20:26 +0000
Subject: [PATCH 01/24] Attempt to use view

---
 src/mdio/segy/_workers.py | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/src/mdio/segy/_workers.py b/src/mdio/segy/_workers.py
index 58f8a390a..7de5fdb38 100644
--- a/src/mdio/segy/_workers.py
+++ b/src/mdio/segy/_workers.py
@@ -138,15 +138,19 @@ def trace_worker(  # noqa: PLR0913
         do_reverse_transforms = True
         worker_variables.append(raw_header_key)
 
-    raw_headers, transformed_headers, traces = get_header_raw_and_transformed(
-        segy_file, live_trace_indexes, do_reverse_transforms=do_reverse_transforms
-    )
+    # raw_headers, transformed_headers, traces = get_header_raw_and_transformed(
+    #     segy_file, live_trace_indexes, do_reverse_transforms=do_reverse_transforms
+    # )
+    from copy import deepcopy  # TODO: Move to head if we need to copy
+    header_pipeline = deepcopy(segy_file.accessors.header_decode_pipeline)
+    traces = segy_file.trace[live_trace_indexes]
     ds_to_write = dataset[worker_variables]
 
     if header_key in worker_variables:
         # Create temporary array for headers with the correct shape
         tmp_headers = np.zeros_like(dataset[header_key])
-        tmp_headers[not_null] = transformed_headers
+        # tmp_headers[not_null] = transformed_headers
+        tmp_headers[not_null] = header_pipeline.apply(traces.header.copy())
         # Create a new Variable object to avoid copying the temporary array
         # The ideal solution is to use `ds_to_write[header_key][:] = tmp_headers`
         # but Xarray appears to be copying memory instead of doing direct assignment.
@@ -157,10 +161,11 @@ def trace_worker(  # noqa: PLR0913
             attrs=ds_to_write[header_key].attrs,
             encoding=ds_to_write[header_key].encoding,  # Not strictly necessary, but safer than not doing it.
         )
-    del transformed_headers  # Manage memory
+    # del transformed_headers  # Manage memory
     if raw_header_key in worker_variables:
         tmp_raw_headers = np.zeros_like(dataset[raw_header_key])
-        tmp_raw_headers[not_null] = raw_headers.view("|V240")
+        # tmp_raw_headers[not_null] = raw_headers.view("|V240")
+        tmp_raw_headers[not_null] = traces.header.view("|V240")
 
         ds_to_write[raw_header_key] = Variable(
             ds_to_write[raw_header_key].dims,
@@ -169,7 +174,7 @@ def trace_worker(  # noqa: PLR0913
             encoding=ds_to_write[raw_header_key].encoding,  # Not strictly necessary, but safer than not doing it.
         )
 
-    del raw_headers  # Manage memory
+    # del raw_headers  # Manage memory
     data_variable = ds_to_write[data_variable_name]
     fill_value = _get_fill_value(ScalarType(data_variable.dtype.name))
     tmp_samples = np.full_like(data_variable, fill_value=fill_value)

From 3bb5fe981f88cf0e785e196fbad83887b1a3dc63 Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Fri, 19 Sep 2025 16:25:03 +0000
Subject: [PATCH 02/24] Add hex-dump and MDIO output reproducer

---
 disaster_recovery_analysis/bootstrap.sh       |  76 +++++++
 .../ingest_both_teapots.py                    |  43 ++++
 disaster_recovery_analysis/src/main.rs        | 200 ++++++++++++++++++
 3 files changed, 319 insertions(+)
 create mode 100755 disaster_recovery_analysis/bootstrap.sh
 create mode 100644 disaster_recovery_analysis/ingest_both_teapots.py
 create mode 100644 disaster_recovery_analysis/src/main.rs

diff --git a/disaster_recovery_analysis/bootstrap.sh b/disaster_recovery_analysis/bootstrap.sh
new file mode 100755
index 000000000..a6557a2bf
--- /dev/null
+++ b/disaster_recovery_analysis/bootstrap.sh
@@ -0,0 +1,76 @@
+#!/bin/bash
+
+set -e  # Exit on any error
+
+echo "=== Zarr Hexdump Bootstrap Script ==="
+echo
+
+# Check if Rust is installed, if not install it
+if ! command -v rustc &> /dev/null; then
+    echo "Rust is not installed. Installing Rust..."
+    curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+    source $HOME/.cargo/env
+    echo "✓ Rust installed successfully"
+fi
+
+echo "✓ Rust is installed ($(rustc --version))"
+
+# Check if Cargo is available
+if ! command -v cargo &> /dev/null; then
+    echo "Sourcing Rust environment..."
+    source $HOME/.cargo/env
+fi
+
+echo "✓ Cargo is available ($(cargo --version))"
+echo
+
+# Install blosc library if not present
+echo "Checking for blosc library..."
+if ! pkg-config --exists blosc; then
+    echo "Installing blosc library..."
+    sudo apt-get update
+    sudo apt-get install -y libblosc-dev pkg-config
+    echo "✓ Blosc library installed"
+else
+    echo "✓ Blosc library already available"
+fi
+echo
+
+# Build the project
+echo "Building the Zarr hexdump tool..."
+if cargo build --release; then
+    echo "✓ Build successful!"
+else
+    echo "✗ Build failed!"
+    exit 1
+fi
+
+echo
+echo "=== Usage ==="
+echo "To hexdump a Zarr array, run:"
+echo "  ./target/release/zarr-hexdump /path/to/your/zarr/array"
+echo
+echo "Or use cargo run:"
+echo "  cargo run --release -- /path/to/your/zarr/array"
+echo
+
+# Check if a path was provided as an argument
+if [ $# -eq 1 ]; then
+    ZARR_PATH="$1"
+    echo "=== Running hexdump on provided path: $ZARR_PATH ==="
+    echo
+    
+    if [ -e "$ZARR_PATH" ]; then
+        ./target/release/zarr-hexdump "$ZARR_PATH"
+    else
+        echo "Error: Path '$ZARR_PATH' does not exist!"
+        exit 1
+    fi
+elif [ $# -gt 1 ]; then
+    echo "Error: Too many arguments provided."
+    echo "Usage: $0 [zarr_array_path]"
+    exit 1
+else
+    echo "No Zarr array path provided. Build completed successfully."
+    echo "Use the commands above to run the hexdump tool."
+fi
diff --git a/disaster_recovery_analysis/ingest_both_teapots.py b/disaster_recovery_analysis/ingest_both_teapots.py
new file mode 100644
index 000000000..04aa52f56
--- /dev/null
+++ b/disaster_recovery_analysis/ingest_both_teapots.py
@@ -0,0 +1,43 @@
+if __name__ == "__main__":
+    import mdio
+    from segy.standards import get_segy_standard
+    from segy.schema import HeaderField, Endianness
+    import os
+    from mdio.builder.template_registry import TemplateRegistry
+
+    import logging
+
+    logging.getLogger("segy").setLevel(logging.DEBUG)
+
+    os.environ["MDIO__IMPORT__CLOUD_NATIVE"] = "true"
+    os.environ["MDIO__IMPORT__CPU_COUNT"] = "16"
+    os.environ["MDIO__DO_RAW_HEADERS"] = "1"
+
+    custom_headers = [
+        HeaderField(name="inline", byte=181, format="int32"),
+        HeaderField(name="crossline", byte=185, format="int32"),
+        HeaderField(name="cdp_x", byte=81, format="int32"),
+        HeaderField(name="cdp_y", byte=85, format="int32"),
+    ]
+
+    big_endian_spec = get_segy_standard(0)
+    big_endian_spec.endianness = Endianness.BIG
+    little_endian_spec = get_segy_standard(0)
+    little_endian_spec.endianness = Endianness.LITTLE
+    big_endian_spec = big_endian_spec.customize(trace_header_fields=custom_headers)
+    little_endian_spec = little_endian_spec.customize(trace_header_fields=custom_headers)
+
+    mdio.segy_to_mdio(
+        segy_spec=big_endian_spec,
+        mdio_template=TemplateRegistry().get("PostStack3DTime"),
+        input_path="filt_mig_IEEE_BigEndian_Rev1.sgy",
+        output_path="filt_mig_IEEE_BigEndian_Rev1.mdio",
+        overwrite=True,
+    )
+    mdio.segy_to_mdio(
+        segy_spec=little_endian_spec,
+        mdio_template=TemplateRegistry().get("PostStack3DTime"),
+        input_path="filt_mig_IEEE_LittleEndian_Rev1.sgy",
+        output_path="filt_mig_IEEE_LittleEndian_Rev1.mdio",
+        overwrite=True,
+    )
\ No newline at end of file
diff --git a/disaster_recovery_analysis/src/main.rs b/disaster_recovery_analysis/src/main.rs
new file mode 100644
index 000000000..974e38089
--- /dev/null
+++ b/disaster_recovery_analysis/src/main.rs
@@ -0,0 +1,200 @@
+use std::env;
+use std::fs;
+use std::path::Path;
+use walkdir::WalkDir;
+fn decompress_blosc(compressed_data: &[u8]) -> Result<Vec<u8>, String> {
+    unsafe {
+        // Get decompressed size first
+        let mut nbytes = 0usize;
+        let mut cbytes = 0usize;
+        let mut blocksize = 0usize;
+        
+        blosc_sys::blosc_cbuffer_sizes(
+            compressed_data.as_ptr() as *const std::ffi::c_void,
+            &mut nbytes as *mut usize,
+            &mut cbytes as *mut usize,
+            &mut blocksize as *mut usize,
+        );
+        
+        if nbytes == 0 {
+            return Err("Invalid compressed data".to_string());
+        }
+        
+        // Allocate output buffer
+        let mut decompressed = vec![0u8; nbytes];
+        
+        // Decompress
+        let result = blosc_sys::blosc_decompress(
+            compressed_data.as_ptr() as *const std::ffi::c_void,
+            decompressed.as_mut_ptr() as *mut std::ffi::c_void,
+            nbytes,
+        );
+        
+        if result < 0 {
+            return Err(format!("Blosc decompression failed with code: {}", result));
+        }
+        
+        decompressed.truncate(result as usize);
+        Ok(decompressed)
+    }
+}
+
+fn print_hexdump(data: &[u8], offset: usize, chunk_name: &str) {
+    println!("=== {} ===", chunk_name);
+    for (i, chunk) in data.chunks(16).enumerate() {
+        let addr = offset + i * 16;
+        
+        // Print address
+        print!("{:08x}  ", addr);
+        
+        // Print hex bytes
+        for (j, &byte) in chunk.iter().enumerate() {
+            if j == 8 {
+                print!(" "); // Extra space in the middle
+            }
+            print!("{:02x} ", byte);
+        }
+        
+        // Pad if chunk is less than 16 bytes
+        if chunk.len() < 16 {
+            for j in chunk.len()..16 {
+                if j == 8 {
+                    print!(" ");
+                }
+                print!("   ");
+            }
+        }
+        
+        // Print ASCII representation
+        print!(" |");
+        for &byte in chunk {
+            if byte >= 32 && byte <= 126 {
+                print!("{}", byte as char);
+            } else {
+                print!(".");
+            }
+        }
+        println!("|");
+    }
+    println!();
+}
+
+fn main() -> Result<(), Box<dyn std::error::Error>> {
+    let args: Vec<String> = env::args().collect();
+    
+    if args.len() != 2 {
+        eprintln!("Usage: {} <zarr_array_path>", args[0]);
+        eprintln!("Example: {} /path/to/zarr/array", args[0]);
+        std::process::exit(1);
+    }
+    
+    let zarr_path = Path::new(&args[1]);
+    
+    // Verify the path exists
+    if !zarr_path.exists() {
+        eprintln!("Error: Path '{}' does not exist", zarr_path.display());
+        std::process::exit(1);
+    }
+    
+    println!("Reading Zarr array from: {}", zarr_path.display());
+    println!("========================================");
+    
+    // Read zarr.json metadata
+    let zarr_json_path = zarr_path.join("zarr.json");
+    if !zarr_json_path.exists() {
+        eprintln!("Error: zarr.json not found in {}", zarr_path.display());
+        std::process::exit(1);
+    }
+    
+    let metadata_content = fs::read_to_string(&zarr_json_path)?;
+    let metadata: serde_json::Value = serde_json::from_str(&metadata_content)?;
+    
+    // Extract information from metadata
+    let shape = metadata["shape"].as_array().unwrap();
+    let chunk_shape = metadata["chunk_grid"]["configuration"]["chunk_shape"].as_array().unwrap();
+    
+    println!("Array shape: {:?}", shape);
+    println!("Chunk shape: {:?}", chunk_shape);
+    println!("Data type: {}", metadata["data_type"]["name"]);
+    if let Some(config) = metadata["data_type"]["configuration"].as_object() {
+        if let Some(length_bytes) = config.get("length_bytes") {
+            println!("Length bytes: {}", length_bytes);
+        }
+    }
+    println!();
+    
+    // Calculate expected chunks based on the metadata we know:
+    // Shape: [345, 188], Chunk shape: [128, 128]
+    // This means we have ceil(345/128) = 3 chunks in dimension 0
+    // and ceil(188/128) = 2 chunks in dimension 1
+    // So we expect chunks: c/0/0, c/0/1, c/1/0, c/1/1, c/2/0, c/2/1
+    
+    let mut chunk_files = Vec::new();
+    
+    // Find all chunk files by walking the directory
+    for entry in WalkDir::new(zarr_path) {
+        let entry = entry?;
+        let path = entry.path();
+        
+        // Look for chunk files (they start with 'c/' in Zarr v3)
+        if path.is_file() {
+            let relative_path = path.strip_prefix(zarr_path)?;
+            let path_str = relative_path.to_string_lossy();
+            
+            if path_str.starts_with("c/") {
+                chunk_files.push((path.to_path_buf(), path_str.to_string()));
+            }
+        }
+    }
+    
+    // Sort chunk files for consistent ordering
+    chunk_files.sort_by(|a, b| a.1.cmp(&b.1));
+    
+    println!("Found {} chunk files:", chunk_files.len());
+    for (_, chunk_name) in &chunk_files {
+        println!("  {}", chunk_name);
+    }
+    println!();
+    
+    let mut total_offset = 0;
+    
+    // Read, decompress, and hexdump each chunk file
+    for (chunk_path, chunk_name) in chunk_files {
+        match fs::read(&chunk_path) {
+            Ok(compressed_data) => {
+                if compressed_data.is_empty() {
+                    println!("=== {} ===", chunk_name);
+                    println!("(empty chunk)");
+                    println!();
+                } else {
+                    println!("Compressed size: {} bytes", compressed_data.len());
+                    
+                    // Decompress the Blosc-compressed data using blosc-sys directly
+                    match decompress_blosc(&compressed_data) {
+                        Ok(decompressed_data) => {
+                            println!("Decompressed size: {} bytes", decompressed_data.len());
+                            print_hexdump(&decompressed_data, total_offset, &chunk_name);
+                            total_offset += decompressed_data.len();
+                        }
+                        Err(e) => {
+                            eprintln!("Error decompressing chunk {}: {}", chunk_name, e);
+                            println!("Showing raw compressed data instead:");
+                            print_hexdump(&compressed_data, total_offset, &format!("{} (compressed)", chunk_name));
+                            total_offset += compressed_data.len();
+                        }
+                    }
+                }
+            }
+            Err(e) => {
+                eprintln!("Error reading chunk {}: {}", chunk_name, e);
+            }
+        }
+    }
+    
+    println!("Total decompressed bytes processed: {}", total_offset);
+    println!();
+    println!("Note: This shows the decompressed array data as it would appear in memory.");
+    println!("Each element is 240 bytes (raw_bytes with length_bytes: 240).");
+    
+    Ok(())
+}

From e48e5f395b3800b668ca18d6eb0114edd4b685ba Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Fri, 19 Sep 2025 21:24:20 +0000
Subject: [PATCH 03/24] Fixes

---
 src/mdio/segy/_workers.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/mdio/segy/_workers.py b/src/mdio/segy/_workers.py
index 7de5fdb38..db5c8aaad 100644
--- a/src/mdio/segy/_workers.py
+++ b/src/mdio/segy/_workers.py
@@ -138,11 +138,9 @@ def trace_worker(  # noqa: PLR0913
         do_reverse_transforms = True
         worker_variables.append(raw_header_key)
 
-    # raw_headers, transformed_headers, traces = get_header_raw_and_transformed(
-    #     segy_file, live_trace_indexes, do_reverse_transforms=do_reverse_transforms
-    # )
     from copy import deepcopy  # TODO: Move to head if we need to copy
     header_pipeline = deepcopy(segy_file.accessors.header_decode_pipeline)
+    segy_file.accessors.header_decode_pipeline.transforms = []
     traces = segy_file.trace[live_trace_indexes]
     ds_to_write = dataset[worker_variables]
 
@@ -164,8 +162,7 @@ def trace_worker(  # noqa: PLR0913
     # del transformed_headers  # Manage memory
     if raw_header_key in worker_variables:
         tmp_raw_headers = np.zeros_like(dataset[raw_header_key])
-        # tmp_raw_headers[not_null] = raw_headers.view("|V240")
-        tmp_raw_headers[not_null] = traces.header.view("|V240")
+        tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header).view("|V240")
 
         ds_to_write[raw_header_key] = Variable(
             ds_to_write[raw_header_key].dims,

From 7dad895a17c3db26ec2e3192456763cc1d8f66f9 Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Fri, 19 Sep 2025 21:24:55 +0000
Subject: [PATCH 04/24] Cleanup

---
 src/mdio/segy/_workers.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/mdio/segy/_workers.py b/src/mdio/segy/_workers.py
index db5c8aaad..d5b951732 100644
--- a/src/mdio/segy/_workers.py
+++ b/src/mdio/segy/_workers.py
@@ -126,16 +126,12 @@ def trace_worker(  # noqa: PLR0913
     header_key = "headers"
     raw_header_key = "raw_headers"
 
-    # Used to disable the reverse transforms if we aren't going to write the raw headers
-    do_reverse_transforms = False
-
     # Get subset of the dataset that has not yet been saved
     # The headers might not be present in the dataset
     worker_variables = [data_variable_name]
     if header_key in dataset.data_vars:  # Keeping the `if` here to allow for more worker configurations
         worker_variables.append(header_key)
     if raw_header_key in dataset.data_vars:
-        do_reverse_transforms = True
         worker_variables.append(raw_header_key)
 
     from copy import deepcopy  # TODO: Move to head if we need to copy

From 8d6e517485768279dfc4f231f622f8ea6c37aa94 Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Mon, 22 Sep 2025 14:00:19 +0000
Subject: [PATCH 05/24] Provide clean disaster recovery interface

---
 src/mdio/segy/_disaster_recovery_wrapper.py | 79 +++++----------------
 src/mdio/segy/_workers.py                   | 18 ++---
 2 files changed, 28 insertions(+), 69 deletions(-)

diff --git a/src/mdio/segy/_disaster_recovery_wrapper.py b/src/mdio/segy/_disaster_recovery_wrapper.py
index ad53a5400..3c2443c93 100644
--- a/src/mdio/segy/_disaster_recovery_wrapper.py
+++ b/src/mdio/segy/_disaster_recovery_wrapper.py
@@ -4,73 +4,32 @@
 
 from typing import TYPE_CHECKING
 
-from segy.schema import Endianness
-from segy.transforms import ByteSwapTransform
-from segy.transforms import IbmFloatTransform
+from copy import deepcopy
+import numpy as np
 
 if TYPE_CHECKING:
     from numpy.typing import NDArray
     from segy import SegyFile
-    from segy.transforms import Transform
-    from segy.transforms import TransformPipeline
 
+class SegyFileTraceDataWrapper:
 
-def _reverse_single_transform(data: NDArray, transform: Transform, endianness: Endianness) -> NDArray:
-    """Reverse a single transform operation."""
-    if isinstance(transform, ByteSwapTransform):
-        # Reverse the endianness conversion
-        if endianness == Endianness.LITTLE:
-            return data
+    def __init__(self, segy_file: SegyFile, indices: int | list[int] | NDArray | slice):
+        self.segy_file = segy_file
+        self.indices = indices
+        self._header_pipeline = deepcopy(segy_file.accessors.header_decode_pipeline)
+        segy_file.accessors.header_decode_pipeline.transforms = []
+        self.traces = segy_file.trace[indices]
 
-        reverse_transform = ByteSwapTransform(Endianness.BIG)
-        return reverse_transform.apply(data)
+    @property
+    def header(self):
+        # The copy is necessary to avoid applying the pipeline to the original header.
+        return self._header_pipeline.apply(self.traces.header.copy())
 
-    # TODO(BrianMichell): #0000 Do we actually need to worry about IBM/IEEE transforms here?
-    if isinstance(transform, IbmFloatTransform):
-        # Reverse IBM float conversion
-        reverse_direction = "to_ibm" if transform.direction == "to_ieee" else "to_ieee"
-        reverse_transform = IbmFloatTransform(reverse_direction, transform.keys)
-        return reverse_transform.apply(data)
 
-    # For unknown transforms, return data unchanged
-    return data
+    @property
+    def raw_header(self):
+        return np.ascontiguousarray(self.traces.header).view("|V240")
 
-
-def get_header_raw_and_transformed(
-    segy_file: SegyFile, indices: int | list[int] | NDArray | slice, do_reverse_transforms: bool = True
-) -> tuple[NDArray | None, NDArray, NDArray]:
-    """Get both raw and transformed header data.
-
-    Args:
-        segy_file: The SegyFile instance
-        indices: Which headers to retrieve
-        do_reverse_transforms: Whether to apply the reverse transform to get raw data
-
-    Returns:
-        Tuple of (raw_headers, transformed_headers, traces)
-    """
-    traces = segy_file.trace[indices]
-    transformed_headers = traces.header
-
-    # Reverse transforms to get raw data
-    if do_reverse_transforms:
-        raw_headers = _reverse_transforms(
-            transformed_headers, segy_file.header.transform_pipeline, segy_file.spec.endianness
-        )
-    else:
-        raw_headers = None
-
-    return raw_headers, transformed_headers, traces
-
-
-def _reverse_transforms(
-    transformed_data: NDArray, transform_pipeline: TransformPipeline, endianness: Endianness
-) -> NDArray:
-    """Reverse the transform pipeline to get raw data."""
-    raw_data = transformed_data.copy() if hasattr(transformed_data, "copy") else transformed_data
-
-    # Apply transforms in reverse order
-    for transform in reversed(transform_pipeline.transforms):
-        raw_data = _reverse_single_transform(raw_data, transform, endianness)
-
-    return raw_data
+    @property
+    def sample(self):
+        return self.traces.sample
diff --git a/src/mdio/segy/_workers.py b/src/mdio/segy/_workers.py
index d5b951732..54671ff22 100644
--- a/src/mdio/segy/_workers.py
+++ b/src/mdio/segy/_workers.py
@@ -12,7 +12,7 @@
 
 from mdio.api.io import to_mdio
 from mdio.builder.schemas.dtype import ScalarType
-from mdio.segy._disaster_recovery_wrapper import get_header_raw_and_transformed
+from mdio.segy._disaster_recovery_wrapper import SegyFileTraceDataWrapper
 
 if TYPE_CHECKING:
     from segy.arrays import HeaderArray
@@ -134,17 +134,18 @@ def trace_worker(  # noqa: PLR0913
     if raw_header_key in dataset.data_vars:
         worker_variables.append(raw_header_key)
 
-    from copy import deepcopy  # TODO: Move to head if we need to copy
-    header_pipeline = deepcopy(segy_file.accessors.header_decode_pipeline)
-    segy_file.accessors.header_decode_pipeline.transforms = []
-    traces = segy_file.trace[live_trace_indexes]
+    # traces = segy_file.trace[live_trace_indexes]
+    # Raw headers are not intended to remain as a feature of the SEGY ingestion.
+    # For that reason, we have wrapped the accessors to provide an interface that can be removed
+    # and not require additional changes to the below code.
+    # NOTE: The `raw_header_key` code block should be removed in full as it will become dead code.
+    traces = SegyFileTraceDataWrapper(segy_file, live_trace_indexes)
     ds_to_write = dataset[worker_variables]
 
     if header_key in worker_variables:
         # Create temporary array for headers with the correct shape
         tmp_headers = np.zeros_like(dataset[header_key])
-        # tmp_headers[not_null] = transformed_headers
-        tmp_headers[not_null] = header_pipeline.apply(traces.header.copy())
+        tmp_headers[not_null] = traces.header
         # Create a new Variable object to avoid copying the temporary array
         # The ideal solution is to use `ds_to_write[header_key][:] = tmp_headers`
         # but Xarray appears to be copying memory instead of doing direct assignment.
@@ -155,10 +156,9 @@ def trace_worker(  # noqa: PLR0913
             attrs=ds_to_write[header_key].attrs,
             encoding=ds_to_write[header_key].encoding,  # Not strictly necessary, but safer than not doing it.
         )
-    # del transformed_headers  # Manage memory
     if raw_header_key in worker_variables:
         tmp_raw_headers = np.zeros_like(dataset[raw_header_key])
-        tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header).view("|V240")
+        tmp_raw_headers[not_null] = traces.raw_header
 
         ds_to_write[raw_header_key] = Variable(
             ds_to_write[raw_header_key].dims,

From d34b795d632dad41f49a61b6af3b9a468cb7573d Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Mon, 22 Sep 2025 15:33:21 +0000
Subject: [PATCH 06/24] Begin work on tests

---
 .../test_segy_import_export_masked.py         |  99 ++++++-
 tests/unit/test_disaster_recovery_wrapper.py  | 267 +++++++-----------
 2 files changed, 190 insertions(+), 176 deletions(-)

diff --git a/tests/integration/test_segy_import_export_masked.py b/tests/integration/test_segy_import_export_masked.py
index 2094ca4fc..2e2083804 100644
--- a/tests/integration/test_segy_import_export_masked.py
+++ b/tests/integration/test_segy_import_export_masked.py
@@ -282,11 +282,16 @@ def generate_selection_mask(selection_conf: SelectionMaskConfig, grid_conf: Grid
 
 
 @pytest.fixture
-def export_masked_path(tmp_path_factory: pytest.TempPathFactory) -> Path:
+def export_masked_path(tmp_path_factory: pytest.TempPathFactory, raw_headers_env: None) -> Path:  # noqa: ARG001
     """Fixture that generates temp directory for export tests."""
+    # Create path suffix based on current raw headers environment variable
+    # raw_headers_env dependency ensures the environment variable is set before this runs
+    raw_headers_enabled = os.getenv("MDIO__DO_RAW_HEADERS") == "1"
+    path_suffix = "with_raw_headers" if raw_headers_enabled else "without_raw_headers"
+    
     if DEBUG_MODE:
-        return Path("TMP/export_masked")
-    return tmp_path_factory.getbasetemp() / "export_masked"
+        return Path(f"TMP/export_masked_{path_suffix}")
+    return tmp_path_factory.getbasetemp() / f"export_masked_{path_suffix}"
 
 
 @pytest.fixture
@@ -300,8 +305,33 @@ def raw_headers_env(request: pytest.FixtureRequest) -> None:
 
     yield
 
-    # Cleanup after test
+    # Cleanup after test - both environment variable and template state
     os.environ.pop("MDIO__DO_RAW_HEADERS", None)
+    
+    # Clean up any template modifications to ensure test isolation
+    from mdio.builder.template_registry import TemplateRegistry
+    registry = TemplateRegistry.get_instance()
+    
+    # Reset any templates that might have been modified with raw headers
+    template_names = ["PostStack2DTime", "PostStack3DTime", "PreStackCdpOffsetGathers2DTime", 
+                     "PreStackCdpOffsetGathers3DTime", "PreStackShotGathers2DTime", 
+                     "PreStackShotGathers3DTime", "PreStackCocaGathers3DTime"]
+    
+    for template_name in template_names:
+        try:
+            template = registry.get(template_name)
+            # Remove raw headers enhancement if present
+            if hasattr(template, "_mdio_raw_headers_enhanced"):
+                delattr(template, "_mdio_raw_headers_enhanced")
+                # The enhancement is applied by monkey-patching _add_variables
+                # We need to restore it to the original method from the class
+                # Since we can't easily restore the exact original, we'll get a fresh instance
+                template_class = type(template)
+                if hasattr(template_class, '_add_variables'):
+                    template._add_variables = template_class._add_variables.__get__(template, template_class)
+        except KeyError:
+            # Template not found, skip
+            continue
 
 
 @pytest.mark.parametrize(
@@ -471,3 +501,64 @@ def test_export_masked(
         # https://github.com/TGSAI/mdio-python/issues/610
         assert_array_equal(actual_sgy.trace[:].header, expected_sgy.trace[expected_trc_idx].header)
         assert_array_equal(actual_sgy.trace[:].sample, expected_sgy.trace[expected_trc_idx].sample)
+
+    def test_raw_headers_byte_preservation(
+        self,
+        test_conf: MaskedExportConfig,
+        export_masked_path: Path,
+        raw_headers_env: None,  # noqa: ARG002
+    ) -> None:
+        """Test that raw headers are preserved byte-for-byte when MDIO__DO_RAW_HEADERS=1."""
+        grid_conf, segy_factory_conf, _, _ = test_conf
+        segy_path = export_masked_path / f"{grid_conf.name}.sgy"
+        mdio_path = export_masked_path / f"{grid_conf.name}.mdio"
+
+        # Open MDIO dataset
+        ds = open_mdio(mdio_path)
+
+        # Check if raw_headers should exist based on environment variable
+        has_raw_headers = "raw_headers" in ds.data_vars
+        if os.getenv("MDIO__DO_RAW_HEADERS") == "1":
+            assert has_raw_headers, "raw_headers should be present when MDIO__DO_RAW_HEADERS=1"
+        else:
+            assert not has_raw_headers, f"raw_headers should not be present when MDIO__DO_RAW_HEADERS is not set\n {ds}"
+            return  # Exit early if raw_headers are not expected
+        
+        # Get data (only if raw_headers exist)
+        raw_headers_data = ds.raw_headers.values
+        trace_mask = ds.trace_mask.values
+        
+        # Verify 240-byte headers
+        assert raw_headers_data.dtype.itemsize == 240, f"Expected 240-byte headers, got {raw_headers_data.dtype.itemsize}"
+        
+        # Read raw bytes directly from SEG-Y file
+        def read_segy_trace_header(trace_index: int) -> bytes:
+            """Read 240-byte trace header directly from SEG-Y file."""
+            with open(segy_path, 'rb') as f:
+                # Skip text (3200) + binary (400) headers = 3600 bytes
+                f.seek(3600)
+                # Each trace: 240 byte header + (num_samples * 4) byte samples
+                trace_size = 240 + (segy_factory_conf.num_samples * 4)
+                trace_offset = trace_index * trace_size
+                f.seek(trace_offset, 1)  # Seek relative to current position
+                return f.read(240)
+        
+        # Compare all valid traces byte-by-byte
+        segy_trace_idx = 0
+        flat_mask = trace_mask.ravel()
+        flat_raw_headers = raw_headers_data.reshape(-1, raw_headers_data.shape[-1])
+        
+        for grid_idx in range(flat_mask.size):
+            if not flat_mask[grid_idx]:
+                continue
+                
+            # Get MDIO header as bytes
+            mdio_header_bytes = np.frombuffer(flat_raw_headers[grid_idx].tobytes(), dtype=np.uint8)
+            
+            # Get SEG-Y header as raw bytes directly from file
+            segy_raw_header_bytes = read_segy_trace_header(segy_trace_idx)
+            segy_header_bytes = np.frombuffer(segy_raw_header_bytes, dtype=np.uint8)
+            
+            # Compare byte-by-byte
+            assert_array_equal(mdio_header_bytes, segy_header_bytes)
+            segy_trace_idx += 1
diff --git a/tests/unit/test_disaster_recovery_wrapper.py b/tests/unit/test_disaster_recovery_wrapper.py
index 9ed5e045d..e4e3e31fa 100644
--- a/tests/unit/test_disaster_recovery_wrapper.py
+++ b/tests/unit/test_disaster_recovery_wrapper.py
@@ -20,7 +20,7 @@
 from segy.schema import SegySpec
 from segy.standards import get_segy_standard
 
-from mdio.segy._disaster_recovery_wrapper import get_header_raw_and_transformed
+from mdio.segy._disaster_recovery_wrapper import SegyFileTraceDataWrapper
 
 if TYPE_CHECKING:
     from numpy.typing import NDArray
@@ -118,27 +118,11 @@ def create_test_segy_file(  # noqa: PLR0913
 
         return spec
 
-    def extract_header_bytes_from_file(
-        self, segy_path: Path, trace_index: int, byte_start: int, byte_length: int
-    ) -> NDArray:
-        """Extract specific bytes from a trace header in the SEGY file."""
-        with segy_path.open("rb") as f:
-            # Skip text header (3200 bytes) + binary header (400 bytes)
-            header_offset = 3600
 
-            # Each trace: 240 byte header + samples
-            trace_size = 240 + SAMPLES_PER_TRACE * 4  # samples * 4 bytes each
-            trace_offset = header_offset + trace_index * trace_size
-
-            f.seek(trace_offset + byte_start - 1)  # SEGY is 1-based
-            header_bytes = f.read(byte_length)
-
-            return np.frombuffer(header_bytes, dtype=np.uint8)
-
-    def test_header_validation_configurations(
+    def test_wrapper_basic_functionality(
         self, temp_dir: Path, basic_segy_spec: SegySpec, segy_config: dict
     ) -> None:
-        """Test header validation with different SEGY configurations."""
+        """Test basic functionality of SegyFileTraceDataWrapper."""
         config_name = segy_config["name"]
         endianness = segy_config["endianness"]
         data_format = segy_config["data_format"]
@@ -161,75 +145,35 @@ def test_header_validation_configurations(
         # Load the SEGY file
         segy_file = SegyFile(segy_path, spec=spec)
 
-        # Test a few traces
-        test_indices = [0, 3, 7]
-
-        for trace_idx in test_indices:
-            # Get raw and transformed headers
-            raw_headers, transformed_headers, traces = get_header_raw_and_transformed(
-                segy_file=segy_file, indices=trace_idx, do_reverse_transforms=True
-            )
-
-            # Extract bytes from disk for inline (bytes 189-192) and crossline (bytes 193-196)
-            inline_bytes_disk = self.extract_header_bytes_from_file(segy_path, trace_idx, 189, 4)
-            crossline_bytes_disk = self.extract_header_bytes_from_file(segy_path, trace_idx, 193, 4)
-
-            # Convert raw headers to bytes for comparison
-            if raw_headers is not None:
-                # Extract from raw headers
-                # Note: We need to extract bytes directly from the structured array to preserve endianness
-                # Getting a scalar and calling .tobytes() loses endianness information
-                if raw_headers.ndim == 0:
-                    # Single trace case
-                    raw_data_bytes = raw_headers.tobytes()
-                    inline_offset = raw_headers.dtype.fields["inline"][1]
-                    crossline_offset = raw_headers.dtype.fields["crossline"][1]
-                    inline_size = raw_headers.dtype.fields["inline"][0].itemsize
-                    crossline_size = raw_headers.dtype.fields["crossline"][0].itemsize
-
-                    raw_inline_bytes = np.frombuffer(
-                        raw_data_bytes[inline_offset : inline_offset + inline_size], dtype=np.uint8
-                    )
-                    raw_crossline_bytes = np.frombuffer(
-                        raw_data_bytes[crossline_offset : crossline_offset + crossline_size], dtype=np.uint8
-                    )
-                else:
-                    # Multiple traces case - this test uses single trace index, so extract that trace
-                    raw_data_bytes = raw_headers[0:1].tobytes()  # Extract first trace
-                    inline_offset = raw_headers.dtype.fields["inline"][1]
-                    crossline_offset = raw_headers.dtype.fields["crossline"][1]
-                    inline_size = raw_headers.dtype.fields["inline"][0].itemsize
-                    crossline_size = raw_headers.dtype.fields["crossline"][0].itemsize
-
-                    raw_inline_bytes = np.frombuffer(
-                        raw_data_bytes[inline_offset : inline_offset + inline_size], dtype=np.uint8
-                    )
-                    raw_crossline_bytes = np.frombuffer(
-                        raw_data_bytes[crossline_offset : crossline_offset + crossline_size], dtype=np.uint8
-                    )
-
-                print(f"Transformed headers: {transformed_headers.tobytes()}")
-                print(f"Raw headers: {raw_headers.tobytes()}")
-                print(f"Inline bytes disk: {inline_bytes_disk.tobytes()}")
-                print(f"Crossline bytes disk: {crossline_bytes_disk.tobytes()}")
-
-                # Compare bytes
-                assert np.array_equal(raw_inline_bytes, inline_bytes_disk), (
-                    f"Inline bytes mismatch for trace {trace_idx} in {config_name}"
-                )
-                assert np.array_equal(raw_crossline_bytes, crossline_bytes_disk), (
-                    f"Crossline bytes mismatch for trace {trace_idx} in {config_name}"
-                )
-
-    def test_header_validation_no_transforms(
+        # Test single trace
+        trace_idx = 3
+        wrapper = SegyFileTraceDataWrapper(segy_file, trace_idx)
+
+        # Test that properties are accessible
+        assert wrapper.header is not None
+        assert wrapper.raw_header is not None
+        assert wrapper.sample is not None
+
+        # Test header properties
+        transformed_header = wrapper.header
+        raw_header = wrapper.raw_header
+
+        # Raw header should be bytes (240 bytes per trace header)
+        assert raw_header.dtype == np.dtype("|V240")
+        
+        # Transformed header should have the expected fields
+        assert "inline" in transformed_header.dtype.names
+        assert "crossline" in transformed_header.dtype.names
+
+    def test_wrapper_with_multiple_traces(
         self, temp_dir: Path, basic_segy_spec: SegySpec, segy_config: dict
     ) -> None:
-        """Test header validation when transforms are disabled."""
+        """Test wrapper with multiple traces."""
         config_name = segy_config["name"]
         endianness = segy_config["endianness"]
         data_format = segy_config["data_format"]
 
-        segy_path = temp_dir / f"test_no_transforms_{config_name}.segy"
+        segy_path = temp_dir / f"test_multiple_{config_name}.segy"
 
         # Create test SEGY file
         num_traces = 5
@@ -247,31 +191,26 @@ def test_header_validation_no_transforms(
         # Load the SEGY file
         segy_file = SegyFile(segy_path, spec=spec)
 
-        # Get headers without reverse transforms
-        raw_headers, transformed_headers, traces = get_header_raw_and_transformed(
-            segy_file=segy_file,
-            indices=slice(None),  # All traces
-            do_reverse_transforms=False,
-        )
+        # Test with list of indices
+        trace_indices = [0, 2, 4]
+        wrapper = SegyFileTraceDataWrapper(segy_file, trace_indices)
 
-        # When transforms are disabled, raw_headers should be None
-        assert raw_headers is None
+        # Test that properties work with multiple traces
+        assert wrapper.header is not None
+        assert wrapper.raw_header is not None
+        assert wrapper.sample is not None
 
-        # Transformed headers should still be available
-        assert transformed_headers is not None
-        assert transformed_headers.size == num_traces
+        # Check that we got the expected number of traces
+        assert wrapper.header.size == len(trace_indices)
+        assert wrapper.raw_header.size == len(trace_indices)
 
-    def test_multiple_traces_validation(self, temp_dir: Path, basic_segy_spec: SegySpec, segy_config: dict) -> None:
-        """Test validation with multiple traces at once."""
+    def test_wrapper_with_slice_indices(self, temp_dir: Path, basic_segy_spec: SegySpec, segy_config: dict) -> None:
+        """Test wrapper with slice indices."""
         config_name = segy_config["name"]
         endianness = segy_config["endianness"]
         data_format = segy_config["data_format"]
 
-        print(f"Config name: {config_name}")
-        print(f"Endianness: {endianness}")
-        print(f"Data format: {data_format}")
-
-        segy_path = temp_dir / f"test_multiple_traces_{config_name}.segy"
+        segy_path = temp_dir / f"test_slice_{config_name}.segy"
 
         # Create test SEGY file with more traces
         num_traces = 25  # 5x5 grid
@@ -291,70 +230,18 @@ def test_multiple_traces_validation(self, temp_dir: Path, basic_segy_spec: SegyS
         # Load the SEGY file
         segy_file = SegyFile(segy_path, spec=spec)
 
-        # Get all traces
-        raw_headers, transformed_headers, traces = get_header_raw_and_transformed(
-            segy_file=segy_file,
-            indices=slice(None),  # All traces
-            do_reverse_transforms=True,
-        )
+        # Test with slice
+        wrapper = SegyFileTraceDataWrapper(segy_file, slice(5, 15))
+
+        # Test that properties work with slice
+        assert wrapper.header is not None
+        assert wrapper.raw_header is not None
+        assert wrapper.sample is not None
 
-        first = True
-
-        # Validate each trace
-        for trace_idx in range(num_traces):
-            # Extract bytes from disk
-            inline_bytes_disk = self.extract_header_bytes_from_file(segy_path, trace_idx, 189, 4)
-            crossline_bytes_disk = self.extract_header_bytes_from_file(segy_path, trace_idx, 193, 4)
-
-            if first:
-                print(raw_headers.dtype)
-                print(raw_headers.shape)
-                first = False
-
-            # Extract from raw headers
-            # Note: We need to extract bytes directly from the structured array to preserve endianness
-            # Getting a scalar and calling .tobytes() loses endianness information
-            if raw_headers.ndim == 0:
-                # Single trace case
-                raw_data_bytes = raw_headers.tobytes()
-                inline_offset = raw_headers.dtype.fields["inline"][1]
-                crossline_offset = raw_headers.dtype.fields["crossline"][1]
-                inline_size = raw_headers.dtype.fields["inline"][0].itemsize
-                crossline_size = raw_headers.dtype.fields["crossline"][0].itemsize
-
-                raw_inline_bytes = np.frombuffer(
-                    raw_data_bytes[inline_offset : inline_offset + inline_size], dtype=np.uint8
-                )
-                raw_crossline_bytes = np.frombuffer(
-                    raw_data_bytes[crossline_offset : crossline_offset + crossline_size], dtype=np.uint8
-                )
-            else:
-                # Multiple traces case
-                raw_data_bytes = raw_headers[trace_idx : trace_idx + 1].tobytes()
-                inline_offset = raw_headers.dtype.fields["inline"][1]
-                crossline_offset = raw_headers.dtype.fields["crossline"][1]
-                inline_size = raw_headers.dtype.fields["inline"][0].itemsize
-                crossline_size = raw_headers.dtype.fields["crossline"][0].itemsize
-
-                raw_inline_bytes = np.frombuffer(
-                    raw_data_bytes[inline_offset : inline_offset + inline_size], dtype=np.uint8
-                )
-                raw_crossline_bytes = np.frombuffer(
-                    raw_data_bytes[crossline_offset : crossline_offset + crossline_size], dtype=np.uint8
-                )
-
-            print(f"Raw inline bytes: {raw_inline_bytes.tobytes()}")
-            print(f"Inline bytes disk: {inline_bytes_disk.tobytes()}")
-            print(f"Raw crossline bytes: {raw_crossline_bytes.tobytes()}")
-            print(f"Crossline bytes disk: {crossline_bytes_disk.tobytes()}")
-
-            # Compare
-            assert np.array_equal(raw_inline_bytes, inline_bytes_disk), (
-                f"Inline bytes mismatch for trace {trace_idx} in {config_name}"
-            )
-            assert np.array_equal(raw_crossline_bytes, crossline_bytes_disk), (
-                f"Crossline bytes mismatch for trace {trace_idx} in {config_name}"
-            )
+        # Check that we got the expected number of traces (10 traces from slice(5, 15))
+        expected_count = 10
+        assert wrapper.header.size == expected_count
+        assert wrapper.raw_header.size == expected_count
 
     @pytest.mark.parametrize(
         "trace_indices",
@@ -367,7 +254,7 @@ def test_multiple_traces_validation(self, temp_dir: Path, basic_segy_spec: SegyS
     def test_different_index_types(
         self, temp_dir: Path, basic_segy_spec: SegySpec, segy_config: dict, trace_indices: int | list[int] | slice
     ) -> None:
-        """Test with different types of trace indices."""
+        """Test wrapper with different types of trace indices."""
         config_name = segy_config["name"]
         endianness = segy_config["endianness"]
         data_format = segy_config["data_format"]
@@ -390,15 +277,13 @@ def test_different_index_types(
         # Load the SEGY file
         segy_file = SegyFile(segy_path, spec=spec)
 
-        # Get headers with different index types
-        raw_headers, transformed_headers, traces = get_header_raw_and_transformed(
-            segy_file=segy_file, indices=trace_indices, do_reverse_transforms=True
-        )
+        # Create wrapper with different index types
+        wrapper = SegyFileTraceDataWrapper(segy_file, trace_indices)
 
         # Basic validation that we got results
-        assert raw_headers is not None
-        assert transformed_headers is not None
-        assert traces is not None
+        assert wrapper.header is not None
+        assert wrapper.raw_header is not None
+        assert wrapper.sample is not None
 
         # Check that the number of results matches expectation
         if isinstance(trace_indices, int):
@@ -410,4 +295,42 @@ def test_different_index_types(
         else:
             expected_count = 1
 
-        assert transformed_headers.size == expected_count
+        assert wrapper.header.size == expected_count
+
+    def test_header_pipeline_preservation(
+        self, temp_dir: Path, basic_segy_spec: SegySpec, segy_config: dict
+    ) -> None:
+        """Test that the wrapper preserves the original header pipeline."""
+        config_name = segy_config["name"]
+        endianness = segy_config["endianness"]
+        data_format = segy_config["data_format"]
+
+        segy_path = temp_dir / f"test_pipeline_{config_name}.segy"
+
+        # Create test SEGY file
+        num_traces = 5
+        samples_per_trace = SAMPLES_PER_TRACE
+
+        spec = self.create_test_segy_file(
+            spec=basic_segy_spec,
+            num_traces=num_traces,
+            samples_per_trace=samples_per_trace,
+            output_path=segy_path,
+            endianness=endianness,
+            data_format=data_format,
+        )
+
+        # Load the SEGY file
+        segy_file = SegyFile(segy_path, spec=spec)
+        
+        # Store original pipeline transforms count
+        original_transforms_count = len(segy_file.accessors.header_decode_pipeline.transforms)
+
+        # Create wrapper
+        wrapper = SegyFileTraceDataWrapper(segy_file, 0)
+
+        # Verify that the original SEGY file's pipeline was modified (transforms cleared)
+        assert len(segy_file.accessors.header_decode_pipeline.transforms) == 0
+        
+        # Verify that the wrapper has its own pipeline with the original transforms
+        assert len(wrapper._header_pipeline.transforms) == original_transforms_count

From accb5e89db61e85d98ad4c7ee4020f2b55338797 Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Mon, 22 Sep 2025 15:45:52 +0000
Subject: [PATCH 07/24] Fix flattening issue

---
 tests/integration/test_segy_import_export_masked.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/integration/test_segy_import_export_masked.py b/tests/integration/test_segy_import_export_masked.py
index 2e2083804..105eef598 100644
--- a/tests/integration/test_segy_import_export_masked.py
+++ b/tests/integration/test_segy_import_export_masked.py
@@ -546,14 +546,15 @@ def read_segy_trace_header(trace_index: int) -> bytes:
         # Compare all valid traces byte-by-byte
         segy_trace_idx = 0
         flat_mask = trace_mask.ravel()
-        flat_raw_headers = raw_headers_data.reshape(-1, raw_headers_data.shape[-1])
+        flat_raw_headers = raw_headers_data.ravel()  # Flatten to 1D array of 240-byte header records
         
         for grid_idx in range(flat_mask.size):
             if not flat_mask[grid_idx]:
                 continue
                 
-            # Get MDIO header as bytes
-            mdio_header_bytes = np.frombuffer(flat_raw_headers[grid_idx].tobytes(), dtype=np.uint8)
+            # Get MDIO header as bytes - convert single header record to bytes
+            header_record = flat_raw_headers[grid_idx]
+            mdio_header_bytes = np.frombuffer(header_record.tobytes(), dtype=np.uint8)
             
             # Get SEG-Y header as raw bytes directly from file
             segy_raw_header_bytes = read_segy_trace_header(segy_trace_idx)

From 360e0860f102c863f9a2e040da739d71c974c2ec Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Mon, 22 Sep 2025 19:35:11 +0000
Subject: [PATCH 08/24] Push for debugging

---
 src/mdio/segy/_disaster_recovery_wrapper.py   |  2 +-
 src/mdio/segy/_workers.py                     | 20 ++++++-
 tests/conftest.py                             |  2 +-
 .../test_segy_import_export_masked.py         | 59 ++++++++++++++++++-
 4 files changed, 77 insertions(+), 6 deletions(-)

diff --git a/src/mdio/segy/_disaster_recovery_wrapper.py b/src/mdio/segy/_disaster_recovery_wrapper.py
index 3c2443c93..8b4afb46f 100644
--- a/src/mdio/segy/_disaster_recovery_wrapper.py
+++ b/src/mdio/segy/_disaster_recovery_wrapper.py
@@ -28,7 +28,7 @@ def header(self):
 
     @property
     def raw_header(self):
-        return np.ascontiguousarray(self.traces.header).view("|V240")
+        return np.ascontiguousarray(self.traces.header.copy()).view("|V240")
 
     @property
     def sample(self):
diff --git a/src/mdio/segy/_workers.py b/src/mdio/segy/_workers.py
index 54671ff22..6dc9ff591 100644
--- a/src/mdio/segy/_workers.py
+++ b/src/mdio/segy/_workers.py
@@ -139,13 +139,19 @@ def trace_worker(  # noqa: PLR0913
     # For that reason, we have wrapped the accessors to provide an interface that can be removed
     # and not require additional changes to the below code.
     # NOTE: The `raw_header_key` code block should be removed in full as it will become dead code.
-    traces = SegyFileTraceDataWrapper(segy_file, live_trace_indexes)
+    # traces = SegyFileTraceDataWrapper(segy_file, live_trace_indexes)
+    from copy import deepcopy
+    header_pipeline = deepcopy(segy_file.accessors.header_decode_pipeline)
+    segy_file.accessors.header_decode_pipeline.transforms = []
+    traces = segy_file.trace[live_trace_indexes]
+
     ds_to_write = dataset[worker_variables]
 
     if header_key in worker_variables:
         # Create temporary array for headers with the correct shape
         tmp_headers = np.zeros_like(dataset[header_key])
-        tmp_headers[not_null] = traces.header
+        # tmp_headers[not_null] = traces.header
+        tmp_headers[not_null] = header_pipeline.apply(traces.header.copy())
         # Create a new Variable object to avoid copying the temporary array
         # The ideal solution is to use `ds_to_write[header_key][:] = tmp_headers`
         # but Xarray appears to be copying memory instead of doing direct assignment.
@@ -158,7 +164,15 @@ def trace_worker(  # noqa: PLR0913
         )
     if raw_header_key in worker_variables:
         tmp_raw_headers = np.zeros_like(dataset[raw_header_key])
-        tmp_raw_headers[not_null] = traces.raw_header
+        # tmp_raw_headers = np.zeros((traces.header.shape[0], 240), dtype=np.)
+        # tmp_raw_headers[not_null] = traces.raw_header
+        np.set_printoptions(threshold=np.inf)
+        # print(traces.header.copy().view("|V240"))
+        # print(len(traces.header.view("|V240")))
+        print(len(traces.header))
+        tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy()).view("|V240")
+        # tmp_raw_headers[not_null] = traces.header.view("|V240")
+        # tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy()).view("|V240")
 
         ds_to_write[raw_header_key] = Variable(
             ds_to_write[raw_header_key].dims,
diff --git a/tests/conftest.py b/tests/conftest.py
index 24bc06ef9..bd2aa664e 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -8,7 +8,7 @@
 
 import pytest
 
-DEBUG_MODE = False
+DEBUG_MODE = True
 
 # Suppress Dask's chunk balancing warning
 warnings.filterwarnings(
diff --git a/tests/integration/test_segy_import_export_masked.py b/tests/integration/test_segy_import_export_masked.py
index 105eef598..a80c5cd4d 100644
--- a/tests/integration/test_segy_import_export_masked.py
+++ b/tests/integration/test_segy_import_export_masked.py
@@ -547,9 +547,13 @@ def read_segy_trace_header(trace_index: int) -> bytes:
         segy_trace_idx = 0
         flat_mask = trace_mask.ravel()
         flat_raw_headers = raw_headers_data.ravel()  # Flatten to 1D array of 240-byte header records
+        print(f"Flat mask shape: {flat_mask.shape}")
+
+        operation = 'w'
         
         for grid_idx in range(flat_mask.size):
             if not flat_mask[grid_idx]:
+                print(f"Skipping trace {grid_idx} because it is masked")
                 continue
                 
             # Get MDIO header as bytes - convert single header record to bytes
@@ -561,5 +565,58 @@ def read_segy_trace_header(trace_index: int) -> bytes:
             segy_header_bytes = np.frombuffer(segy_raw_header_bytes, dtype=np.uint8)
             
             # Compare byte-by-byte
-            assert_array_equal(mdio_header_bytes, segy_header_bytes)
+            # Write hexdumps to separate files for analysis
+            def hexdump_to_string(data: bytes, title: str) -> str:
+                """Create hexdump string."""
+                lines = [f"{title}", "=" * len(title), ""]
+                 
+                for i in range(0, len(data), 16):
+                    # Address
+                    addr = i
+                    hex_part = ""
+                    ascii_part = ""
+                     
+                    # Process 16 bytes at a time
+                    for j in range(16):
+                        if i + j < len(data):
+                            byte_val = data[i + j]
+                            hex_part += f"{byte_val:02x} "
+                            ascii_part += chr(byte_val) if 32 <= byte_val <= 126 else "."
+                        else:
+                            hex_part += "   "
+                            ascii_part += " "
+                     
+                    lines.append(f"{addr:08x}: {hex_part} |{ascii_part}|")
+                 
+                return "\n".join(lines)
+             
+            # Generate filenames for this test case
+            segy_filename = f"segy_headers_{grid_conf.name}.txt"
+            mdio_filename = f"mdio_headers_{grid_conf.name}.txt"
+             
+            # Append SEG-Y hexdump to file
+            with open(segy_filename, operation) as f:
+                if segy_trace_idx == 0:
+                    f.write("")  # Start fresh for first trace
+                else:
+                    f.write("\n\n")  # Add spacing between traces
+                f.write(hexdump_to_string(segy_header_bytes, 
+                                        f"SEG-Y Header - {grid_conf.name} Trace {segy_trace_idx} (240 bytes)"))
+             
+            # Append MDIO hexdump to file  
+            with open(mdio_filename, operation) as f:
+                if segy_trace_idx == 0:
+                    f.write("")  # Start fresh for first trace
+                else:
+                    f.write("\n\n")  # Add spacing between traces
+                f.write(hexdump_to_string(mdio_header_bytes,
+                                        f"MDIO Raw Header - {grid_conf.name} Trace {segy_trace_idx} (240 bytes)"))
+            operation = 'a'
+             
+            if segy_trace_idx == 0:
+                print(f"\nHeader hexdumps being written for {grid_conf.name}:")
+                print(f"  SEG-Y: {segy_filename}")
+                print(f"  MDIO:  {mdio_filename}")
+                
+            
             segy_trace_idx += 1

From 5aa44600620c1fe2cf90a68d7a4292d9ccc2487e Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Mon, 22 Sep 2025 21:09:02 +0000
Subject: [PATCH 09/24] Numpy updates

---
 pyproject.toml                                |   1 +
 src/mdio/segy/_workers.py                     |   7 -
 tests/conftest.py                             |   2 +-
 .../test_segy_import_export_masked.py         |  88 +--
 uv.lock                                       | 679 +++++++++---------
 5 files changed, 399 insertions(+), 378 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 76077ee8a..5056dc10a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,6 +22,7 @@ dependencies = [
     "click-params>=0.5.0",
     "dask>=2025.9.0",
     "fsspec>=2025.9.0",
+    "numpy>=2.3.3",
     "pint>=0.25.0",
     "psutil>=7.0.0",
     "pydantic>=2.11.9",
diff --git a/src/mdio/segy/_workers.py b/src/mdio/segy/_workers.py
index 6dc9ff591..b46e29f1f 100644
--- a/src/mdio/segy/_workers.py
+++ b/src/mdio/segy/_workers.py
@@ -164,15 +164,8 @@ def trace_worker(  # noqa: PLR0913
         )
     if raw_header_key in worker_variables:
         tmp_raw_headers = np.zeros_like(dataset[raw_header_key])
-        # tmp_raw_headers = np.zeros((traces.header.shape[0], 240), dtype=np.)
         # tmp_raw_headers[not_null] = traces.raw_header
-        np.set_printoptions(threshold=np.inf)
-        # print(traces.header.copy().view("|V240"))
-        # print(len(traces.header.view("|V240")))
-        print(len(traces.header))
         tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy()).view("|V240")
-        # tmp_raw_headers[not_null] = traces.header.view("|V240")
-        # tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy()).view("|V240")
 
         ds_to_write[raw_header_key] = Variable(
             ds_to_write[raw_header_key].dims,
diff --git a/tests/conftest.py b/tests/conftest.py
index bd2aa664e..24bc06ef9 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -8,7 +8,7 @@
 
 import pytest
 
-DEBUG_MODE = True
+DEBUG_MODE = False
 
 # Suppress Dask's chunk balancing warning
 warnings.filterwarnings(
diff --git a/tests/integration/test_segy_import_export_masked.py b/tests/integration/test_segy_import_export_masked.py
index a80c5cd4d..b58c40688 100644
--- a/tests/integration/test_segy_import_export_masked.py
+++ b/tests/integration/test_segy_import_export_masked.py
@@ -563,60 +563,62 @@ def read_segy_trace_header(trace_index: int) -> bytes:
             # Get SEG-Y header as raw bytes directly from file
             segy_raw_header_bytes = read_segy_trace_header(segy_trace_idx)
             segy_header_bytes = np.frombuffer(segy_raw_header_bytes, dtype=np.uint8)
+
+            assert_array_equal(mdio_header_bytes, segy_header_bytes)
             
             # Compare byte-by-byte
             # Write hexdumps to separate files for analysis
-            def hexdump_to_string(data: bytes, title: str) -> str:
-                """Create hexdump string."""
-                lines = [f"{title}", "=" * len(title), ""]
+            # def hexdump_to_string(data: bytes, title: str) -> str:
+            #     """Create hexdump string."""
+            #     lines = [f"{title}", "=" * len(title), ""]
                  
-                for i in range(0, len(data), 16):
-                    # Address
-                    addr = i
-                    hex_part = ""
-                    ascii_part = ""
+            #     for i in range(0, len(data), 16):
+            #         # Address
+            #         addr = i
+            #         hex_part = ""
+            #         ascii_part = ""
                      
-                    # Process 16 bytes at a time
-                    for j in range(16):
-                        if i + j < len(data):
-                            byte_val = data[i + j]
-                            hex_part += f"{byte_val:02x} "
-                            ascii_part += chr(byte_val) if 32 <= byte_val <= 126 else "."
-                        else:
-                            hex_part += "   "
-                            ascii_part += " "
+            #         # Process 16 bytes at a time
+            #         for j in range(16):
+            #             if i + j < len(data):
+            #                 byte_val = data[i + j]
+            #                 hex_part += f"{byte_val:02x} "
+            #                 ascii_part += chr(byte_val) if 32 <= byte_val <= 126 else "."
+            #             else:
+            #                 hex_part += "   "
+            #                 ascii_part += " "
                      
-                    lines.append(f"{addr:08x}: {hex_part} |{ascii_part}|")
+            #         lines.append(f"{addr:08x}: {hex_part} |{ascii_part}|")
                  
-                return "\n".join(lines)
+            #     return "\n".join(lines)
              
-            # Generate filenames for this test case
-            segy_filename = f"segy_headers_{grid_conf.name}.txt"
-            mdio_filename = f"mdio_headers_{grid_conf.name}.txt"
+            # # Generate filenames for this test case
+            # segy_filename = f"segy_headers_{grid_conf.name}.txt"
+            # mdio_filename = f"mdio_headers_{grid_conf.name}.txt"
              
-            # Append SEG-Y hexdump to file
-            with open(segy_filename, operation) as f:
-                if segy_trace_idx == 0:
-                    f.write("")  # Start fresh for first trace
-                else:
-                    f.write("\n\n")  # Add spacing between traces
-                f.write(hexdump_to_string(segy_header_bytes, 
-                                        f"SEG-Y Header - {grid_conf.name} Trace {segy_trace_idx} (240 bytes)"))
+            # # Append SEG-Y hexdump to file
+            # with open(segy_filename, operation) as f:
+            #     if segy_trace_idx == 0:
+            #         f.write("")  # Start fresh for first trace
+            #     else:
+            #         f.write("\n\n")  # Add spacing between traces
+            #     f.write(hexdump_to_string(segy_header_bytes, 
+            #                             f"SEG-Y Header - {grid_conf.name} Trace {segy_trace_idx} (240 bytes)"))
              
-            # Append MDIO hexdump to file  
-            with open(mdio_filename, operation) as f:
-                if segy_trace_idx == 0:
-                    f.write("")  # Start fresh for first trace
-                else:
-                    f.write("\n\n")  # Add spacing between traces
-                f.write(hexdump_to_string(mdio_header_bytes,
-                                        f"MDIO Raw Header - {grid_conf.name} Trace {segy_trace_idx} (240 bytes)"))
-            operation = 'a'
+            # # Append MDIO hexdump to file  
+            # with open(mdio_filename, operation) as f:
+            #     if segy_trace_idx == 0:
+            #         f.write("")  # Start fresh for first trace
+            #     else:
+            #         f.write("\n\n")  # Add spacing between traces
+            #     f.write(hexdump_to_string(mdio_header_bytes,
+            #                             f"MDIO Raw Header - {grid_conf.name} Trace {segy_trace_idx} (240 bytes)"))
+            # operation = 'a'
              
-            if segy_trace_idx == 0:
-                print(f"\nHeader hexdumps being written for {grid_conf.name}:")
-                print(f"  SEG-Y: {segy_filename}")
-                print(f"  MDIO:  {mdio_filename}")
+            # if segy_trace_idx == 0:
+            #     print(f"\nHeader hexdumps being written for {grid_conf.name}:")
+            #     print(f"  SEG-Y: {segy_filename}")
+            #     print(f"  MDIO:  {mdio_filename}")
                 
             
             segy_trace_idx += 1
diff --git a/uv.lock b/uv.lock
index 7cd4464d3..5c36f5df2 100644
--- a/uv.lock
+++ b/uv.lock
@@ -460,14 +460,14 @@ wheels = [
 
 [[package]]
 name = "click"
-version = "8.2.1"
+version = "8.3.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "colorama", marker = "sys_platform == 'win32'" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/60/6c/8ca2efa64cf75a977a0d7fac081354553ebe483345c734fb6b6515d96bbc/click-8.2.1.tar.gz", hash = "sha256:27c491cc05d968d271d5a1db13e3b5a184636d9d930f148c50b038f0d0646202", size = 286342, upload-time = "2025-05-20T23:19:49.832Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/46/61/de6cd827efad202d7057d93e0fed9294b96952e188f7384832791c7b2254/click-8.3.0.tar.gz", hash = "sha256:e7b8232224eba16f4ebe410c25ced9f7875cb5f3263ffc93cc3e8da705e229c4", size = 276943, upload-time = "2025-09-18T17:32:23.696Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/85/32/10bb5764d90a8eee674e9dc6f4db6a0ab47c8c4d0d83c27f7c39ac415a4d/click-8.2.1-py3-none-any.whl", hash = "sha256:61a3265b914e850b85317d0b3109c7f8cd35a670f963866005d6ef1d5175a12b", size = 102215, upload-time = "2025-05-20T23:19:47.796Z" },
+    { url = "https://files.pythonhosted.org/packages/db/d3/9dcc0f5797f070ec8edf30fbadfb200e71d9db6b84d211e3b2085a7589a0/click-8.3.0-py3-none-any.whl", hash = "sha256:9b9f285302c6e3064f4330c05f05b81945b2a39544279343e6e7c5f27a9baddc", size = 107295, upload-time = "2025-09-18T17:32:22.42Z" },
 ]
 
 [[package]]
@@ -573,55 +573,63 @@ wheels = [
 
 [[package]]
 name = "coverage"
-version = "7.10.6"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/14/70/025b179c993f019105b79575ac6edb5e084fb0f0e63f15cdebef4e454fb5/coverage-7.10.6.tar.gz", hash = "sha256:f644a3ae5933a552a29dbb9aa2f90c677a875f80ebea028e5a52a4f429044b90", size = 823736, upload-time = "2025-08-29T15:35:16.668Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/d4/16/2bea27e212c4980753d6d563a0803c150edeaaddb0771a50d2afc410a261/coverage-7.10.6-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:c706db3cabb7ceef779de68270150665e710b46d56372455cd741184f3868d8f", size = 217129, upload-time = "2025-08-29T15:33:13.575Z" },
-    { url = "https://files.pythonhosted.org/packages/2a/51/e7159e068831ab37e31aac0969d47b8c5ee25b7d307b51e310ec34869315/coverage-7.10.6-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:8e0c38dc289e0508ef68ec95834cb5d2e96fdbe792eaccaa1bccac3966bbadcc", size = 217532, upload-time = "2025-08-29T15:33:14.872Z" },
-    { url = "https://files.pythonhosted.org/packages/e7/c0/246ccbea53d6099325d25cd208df94ea435cd55f0db38099dd721efc7a1f/coverage-7.10.6-cp311-cp311-manylinux1_i686.manylinux_2_28_i686.manylinux_2_5_i686.whl", hash = "sha256:752a3005a1ded28f2f3a6e8787e24f28d6abe176ca64677bcd8d53d6fe2ec08a", size = 247931, upload-time = "2025-08-29T15:33:16.142Z" },
-    { url = "https://files.pythonhosted.org/packages/7d/fb/7435ef8ab9b2594a6e3f58505cc30e98ae8b33265d844007737946c59389/coverage-7.10.6-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl", hash = "sha256:689920ecfd60f992cafca4f5477d55720466ad2c7fa29bb56ac8d44a1ac2b47a", size = 249864, upload-time = "2025-08-29T15:33:17.434Z" },
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-    { url = "https://files.pythonhosted.org/packages/e0/a3/d3d4fd394a10b1256f9dccb2fe0ddd125fc575d7c437b1c70df050f14176/zarr-3.1.2-py3-none-any.whl", hash = "sha256:c3e180f53ee0ef91b86f7feff6f9dd381ddd1b512d1a46580530966a493387b6", size = 261041, upload-time = "2025-08-25T15:32:29.522Z" },
+    { url = "https://files.pythonhosted.org/packages/1a/71/9de7229515a53d1cc5705ca9c411530f711a2242f962214d9dbfe2741aa4/zarr-3.1.3-py3-none-any.whl", hash = "sha256:45f67f87f65f14fa453f99dd8110a5936b7ac69f3a21981d33e90407c80c302a", size = 276427, upload-time = "2025-09-18T19:32:40.042Z" },
 ]
 
 [[package]]

From 93292d1747ba52208e6012b5a0bf5fff83ce4330 Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Tue, 23 Sep 2025 21:35:22 +0000
Subject: [PATCH 10/24] Testing

---
 src/mdio/segy/_workers.py | 79 +++++++++++++++++++++++++++++++++------
 1 file changed, 68 insertions(+), 11 deletions(-)

diff --git a/src/mdio/segy/_workers.py b/src/mdio/segy/_workers.py
index 0fefa74ef..8d4af5f46 100644
--- a/src/mdio/segy/_workers.py
+++ b/src/mdio/segy/_workers.py
@@ -147,6 +147,74 @@ def trace_worker(  # noqa: PLR0913
 
     ds_to_write = dataset[worker_variables]
 
+    if raw_header_key in worker_variables:
+        # from segy.schema import HeaderField, ScalarType
+        from segy.schema import HeaderField
+        from segy.schema import ScalarType as ScalarType2
+
+        new_spec = deepcopy(segy_file.spec)
+        new_spec.trace.header.fields = []
+        new_fields = []
+
+        for i in range(240):
+            new_fields.append(HeaderField(name=f"Field_{i}", format=ScalarType.UINT8, byte=i+1))
+
+        # # new_spec.trace.header.fields = new_fields
+        new_spec = new_spec.customize(trace_header_fields=new_fields)
+        updated_segy_file = SegyFile(segy_file.url, spec=new_spec)
+        updated_traces = updated_segy_file.trace[live_trace_indexes]
+
+        tmp_raw_headers = np.zeros_like(dataset[raw_header_key])
+
+
+        # _foo = traces.tobytes()[:240]
+
+        # _asContiguousCopy = np.ascontiguousarray(traces.header.copy()).view("|V240")
+        # _asContiguousCopy1 = _asContiguousCopy[0]
+
+        # _asContiguousNoCopy = np.ascontiguousarray(traces.header).view("|V240")
+        # _asContiguousNoCopy1 = _asContiguousNoCopy[0]
+
+        # _asArrayCopy = traces.header.copy().view("|V240")
+        # _asArrayCopy1 = _asArrayCopy[0]
+
+        # _asArrayNoCopy = traces.header.view("|V240")
+        # _asArrayNoCopy1 = _asArrayNoCopy[0]
+
+        # _fo = type(traces.header)
+
+        # _aahhhhhhh = segy_file.header[0]
+
+    
+
+        # _asBytes = traces.header.tobytes()
+        # _are_equal = _foo == _asBytes[:240]
+        # _asBytesLen = len(_asBytes)
+        # _asContiguousBytes = np.ascontiguousarray(traces.header).tobytes()
+        # _asContiguousBytesLen = len(_asContiguousBytes)
+        # _asContiguousBytesView = np.ascontiguousarray(traces.header[0]).tobytes().view("|V240")
+        # _asBuffer = memoryview(traces.header)
+
+
+        # _type = traces.header.dtype
+
+        # tmp_raw_headers[not_null] = traces.raw_header
+        # tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy()).view("|V240")
+        # tmp_raw_headers[not_null] = _asContiguousBytes
+        # tmp_raw_headers[not_null] = _asBytes
+        # tmp_raw_headers[not_null] = traces.header.view("|V240")
+        # tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy()).view("|V240")  # Leaks numpy metadata
+        
+        
+        tmp_raw_headers[not_null] = updated_traces.header.view("|V240")
+
+        ds_to_write[raw_header_key] = Variable(
+            ds_to_write[raw_header_key].dims,
+            tmp_raw_headers,
+            attrs=ds_to_write[raw_header_key].attrs,
+            encoding=ds_to_write[raw_header_key].encoding,  # Not strictly necessary, but safer than not doing it.
+        )
+
     if header_key in worker_variables:
         # TODO(BrianMichell): Implement this better so that we can enable fill values without changing the code
         # https://github.com/TGSAI/mdio-python/issues/584
@@ -164,17 +232,6 @@ def trace_worker(  # noqa: PLR0913
             attrs=ds_to_write[header_key].attrs,
             encoding=ds_to_write[header_key].encoding,  # Not strictly necessary, but safer than not doing it.
         )
-    if raw_header_key in worker_variables:
-        tmp_raw_headers = np.zeros_like(dataset[raw_header_key])
-        # tmp_raw_headers[not_null] = traces.raw_header
-        tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy()).view("|V240")
-
-        ds_to_write[raw_header_key] = Variable(
-            ds_to_write[raw_header_key].dims,
-            tmp_raw_headers,
-            attrs=ds_to_write[raw_header_key].attrs,
-            encoding=ds_to_write[raw_header_key].encoding,  # Not strictly necessary, but safer than not doing it.
-        )
 
     # del raw_headers  # Manage memory
     data_variable = ds_to_write[data_variable_name]

From d0c32b09b3acd2c48a20b5ef03f0a94e75820a2f Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Wed, 24 Sep 2025 15:00:19 +0000
Subject: [PATCH 11/24] Working end-to-end examples

---
 src/mdio/converters/segy.py                   | 44 +++++++++++++++++++
 src/mdio/segy/_workers.py                     | 25 ++---------
 .../test_segy_import_export_masked.py         |  1 -
 3 files changed, 47 insertions(+), 23 deletions(-)

diff --git a/src/mdio/converters/segy.py b/src/mdio/converters/segy.py
index a96761c3c..3d99fa61c 100644
--- a/src/mdio/converters/segy.py
+++ b/src/mdio/converters/segy.py
@@ -12,6 +12,8 @@
 from segy.config import SegySettings
 from segy.standards.codes import MeasurementSystem as segy_MeasurementSystem
 from segy.standards.fields.trace import Rev0 as TraceHeaderFieldsRev0
+from segy.schema import HeaderField
+from segy.schema import ScalarType as ScalarType2
 
 from mdio.api.io import _normalize_path
 from mdio.api.io import to_mdio
@@ -340,6 +342,45 @@ def _add_grid_override_to_metadata(dataset: Dataset, grid_overrides: dict[str, A
     if grid_overrides is not None:
         dataset.metadata.attributes["gridOverrides"] = grid_overrides
 
+def _scalar_to_size(scalar: ScalarType2) -> int:
+    if scalar == ScalarType2.UINT8:
+        return 1
+    elif scalar == ScalarType2.UINT16:
+        return 2
+    elif scalar == ScalarType2.UINT32:
+        return 4
+    elif scalar == ScalarType2.UINT64:
+        return 8
+    elif scalar == ScalarType2.INT8:
+        return 1
+    elif scalar == ScalarType2.INT16:
+        return 2
+    elif scalar == ScalarType2.INT32:
+        return 4
+    elif scalar == ScalarType2.INT64:
+        return 8
+    elif scalar == ScalarType2.FLOAT32:
+        return 4
+    elif scalar == ScalarType2.FLOAT64:
+        return 8
+    elif scalar == ScalarType2.FLOAT16:
+        return 2
+    elif scalar == ScalarType2.STRING8:
+        return 8
+    else:
+        raise ValueError(f"Invalid scalar type: {scalar}")
+
+def _customize_segy_spec(segy_spec: SegySpec) -> SegySpec:
+    assigned_bytes = []
+    for field in segy_spec.trace.header.fields:
+        byte = field.byte-1
+        for i in range(byte, byte + _scalar_to_size(field.format)):
+            assigned_bytes.append(i)
+    unassigned_bytes = [i for i in range(240) if i not in assigned_bytes]
+    field_to_customize = [HeaderField(name=f"Field_{i}", format=ScalarType.UINT8, byte=i+1) for i in unassigned_bytes]
+    segy_spec = segy_spec.customize(trace_header_fields=field_to_customize)
+    return segy_spec
+
 
 def _add_raw_headers_to_template(mdio_template: AbstractDatasetTemplate) -> AbstractDatasetTemplate:
     """Add raw headers capability to the MDIO template by monkey-patching its _add_variables method.
@@ -421,6 +462,9 @@ def segy_to_mdio(  # noqa PLR0913
     input_path = _normalize_path(input_path)
     output_path = _normalize_path(output_path)
 
+    if os.getenv("MDIO__DO_RAW_HEADERS") == "1":
+        segy_spec = _customize_segy_spec(segy_spec)
+
     if not overwrite and output_path.exists():
         err = f"Output location '{output_path.as_posix()}' exists. Set `overwrite=True` if intended."
         raise FileExistsError(err)
diff --git a/src/mdio/segy/_workers.py b/src/mdio/segy/_workers.py
index 8d4af5f46..5c82b4653 100644
--- a/src/mdio/segy/_workers.py
+++ b/src/mdio/segy/_workers.py
@@ -148,25 +148,8 @@ def trace_worker(  # noqa: PLR0913
     ds_to_write = dataset[worker_variables]
 
     if raw_header_key in worker_variables:
-        # from segy.schema import HeaderField, ScalarType
-        from segy.schema import HeaderField
-        from segy.schema import ScalarType as ScalarType2
-
-        new_spec = deepcopy(segy_file.spec)
-        new_spec.trace.header.fields = []
-        new_fields = []
-
-        for i in range(240):
-            new_fields.append(HeaderField(name=f"Field_{i}", format=ScalarType.UINT8, byte=i+1))
-
-        # # new_spec.trace.header.fields = new_fields
-        new_spec = new_spec.customize(trace_header_fields=new_fields)
-        updated_segy_file = SegyFile(segy_file.url, spec=new_spec)
-        updated_traces = updated_segy_file.trace[live_trace_indexes]
-
         tmp_raw_headers = np.zeros_like(dataset[raw_header_key])
 
-
         # _foo = traces.tobytes()[:240]
 
         # _asContiguousCopy = np.ascontiguousarray(traces.header.copy()).view("|V240")
@@ -185,8 +168,6 @@ def trace_worker(  # noqa: PLR0913
 
         # _aahhhhhhh = segy_file.header[0]
 
-    
-
         # _asBytes = traces.header.tobytes()
         # _are_equal = _foo == _asBytes[:240]
         # _asBytesLen = len(_asBytes)
@@ -195,18 +176,18 @@ def trace_worker(  # noqa: PLR0913
         # _asContiguousBytesView = np.ascontiguousarray(traces.header[0]).tobytes().view("|V240")
         # _asBuffer = memoryview(traces.header)
 
-
         # _type = traces.header.dtype
 
         # tmp_raw_headers[not_null] = traces.raw_header
-        # tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy()).view("|V240")
+        # tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy(order="C")).view("|V240")
+        tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy()).view("|V240")
         # tmp_raw_headers[not_null] = _asContiguousBytes
         # tmp_raw_headers[not_null] = _asBytes
         # tmp_raw_headers[not_null] = traces.header.view("|V240")
         # tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy()).view("|V240")  # Leaks numpy metadata
         
         
-        tmp_raw_headers[not_null] = updated_traces.header.view("|V240")
+        # tmp_raw_headers[not_null] = updated_traces.header.view("|V240")
 
         ds_to_write[raw_header_key] = Variable(
             ds_to_write[raw_header_key].dims,
diff --git a/tests/integration/test_segy_import_export_masked.py b/tests/integration/test_segy_import_export_masked.py
index b58c40688..3e96e8a63 100644
--- a/tests/integration/test_segy_import_export_masked.py
+++ b/tests/integration/test_segy_import_export_masked.py
@@ -547,7 +547,6 @@ def read_segy_trace_header(trace_index: int) -> bytes:
         segy_trace_idx = 0
         flat_mask = trace_mask.ravel()
         flat_raw_headers = raw_headers_data.ravel()  # Flatten to 1D array of 240-byte header records
-        print(f"Flat mask shape: {flat_mask.shape}")
 
         operation = 'w'
         

From 065280b7cbc0e07f3d9d987cc706521db7706354 Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Wed, 24 Sep 2025 16:20:39 +0000
Subject: [PATCH 12/24] Cleanup

---
 src/mdio/segy/_workers.py | 39 ---------------------------------------
 1 file changed, 39 deletions(-)

diff --git a/src/mdio/segy/_workers.py b/src/mdio/segy/_workers.py
index 5c82b4653..6ec17d7df 100644
--- a/src/mdio/segy/_workers.py
+++ b/src/mdio/segy/_workers.py
@@ -149,45 +149,7 @@ def trace_worker(  # noqa: PLR0913
 
     if raw_header_key in worker_variables:
         tmp_raw_headers = np.zeros_like(dataset[raw_header_key])
-
-        # _foo = traces.tobytes()[:240]
-
-        # _asContiguousCopy = np.ascontiguousarray(traces.header.copy()).view("|V240")
-        # _asContiguousCopy1 = _asContiguousCopy[0]
-
-        # _asContiguousNoCopy = np.ascontiguousarray(traces.header).view("|V240")
-        # _asContiguousNoCopy1 = _asContiguousNoCopy[0]
-
-        # _asArrayCopy = traces.header.copy().view("|V240")
-        # _asArrayCopy1 = _asArrayCopy[0]
-
-        # _asArrayNoCopy = traces.header.view("|V240")
-        # _asArrayNoCopy1 = _asArrayNoCopy[0]
-
-        # _fo = type(traces.header)
-
-        # _aahhhhhhh = segy_file.header[0]
-
-        # _asBytes = traces.header.tobytes()
-        # _are_equal = _foo == _asBytes[:240]
-        # _asBytesLen = len(_asBytes)
-        # _asContiguousBytes = np.ascontiguousarray(traces.header).tobytes()
-        # _asContiguousBytesLen = len(_asContiguousBytes)
-        # _asContiguousBytesView = np.ascontiguousarray(traces.header[0]).tobytes().view("|V240")
-        # _asBuffer = memoryview(traces.header)
-
-        # _type = traces.header.dtype
-
-        # tmp_raw_headers[not_null] = traces.raw_header
-        # tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy(order="C")).view("|V240")
         tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy()).view("|V240")
-        # tmp_raw_headers[not_null] = _asContiguousBytes
-        # tmp_raw_headers[not_null] = _asBytes
-        # tmp_raw_headers[not_null] = traces.header.view("|V240")
-        # tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy()).view("|V240")  # Leaks numpy metadata
-        
-        
-        # tmp_raw_headers[not_null] = updated_traces.header.view("|V240")
 
         ds_to_write[raw_header_key] = Variable(
             ds_to_write[raw_header_key].dims,
@@ -214,7 +176,6 @@ def trace_worker(  # noqa: PLR0913
             encoding=ds_to_write[header_key].encoding,  # Not strictly necessary, but safer than not doing it.
         )
 
-    # del raw_headers  # Manage memory
     data_variable = ds_to_write[data_variable_name]
     fill_value = _get_fill_value(ScalarType(data_variable.dtype.name))
     tmp_samples = np.full_like(data_variable, fill_value=fill_value)

From 5a041a468dc7517eb02782009794df5f17fd3dd6 Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Wed, 24 Sep 2025 16:36:12 +0000
Subject: [PATCH 13/24] Bandaid fix

---
 src/mdio/converters/segy.py | 10 ++++++---
 src/mdio/segy/creation.py   | 41 +++++++++++++++++++++++++++++++++++--
 2 files changed, 46 insertions(+), 5 deletions(-)

diff --git a/src/mdio/converters/segy.py b/src/mdio/converters/segy.py
index 3d99fa61c..50e020127 100644
--- a/src/mdio/converters/segy.py
+++ b/src/mdio/converters/segy.py
@@ -371,15 +371,19 @@ def _scalar_to_size(scalar: ScalarType2) -> int:
         raise ValueError(f"Invalid scalar type: {scalar}")
 
 def _customize_segy_spec(segy_spec: SegySpec) -> SegySpec:
+    from copy import deepcopy
     assigned_bytes = []
+
+    ret = deepcopy(segy_spec)
+
     for field in segy_spec.trace.header.fields:
         byte = field.byte-1
         for i in range(byte, byte + _scalar_to_size(field.format)):
             assigned_bytes.append(i)
     unassigned_bytes = [i for i in range(240) if i not in assigned_bytes]
-    field_to_customize = [HeaderField(name=f"Field_{i}", format=ScalarType.UINT8, byte=i+1) for i in unassigned_bytes]
-    segy_spec = segy_spec.customize(trace_header_fields=field_to_customize)
-    return segy_spec
+    field_to_customize = [HeaderField(name=f"__MDIO_RAW_UNSPECIFIED_Field_{i}", format=ScalarType.UINT8, byte=i+1) for i in unassigned_bytes]
+    ret = ret.customize(trace_header_fields=field_to_customize)
+    return ret
 
 
 def _add_raw_headers_to_template(mdio_template: AbstractDatasetTemplate) -> AbstractDatasetTemplate:
diff --git a/src/mdio/segy/creation.py b/src/mdio/segy/creation.py
index 8b10ad486..81cfd13ae 100644
--- a/src/mdio/segy/creation.py
+++ b/src/mdio/segy/creation.py
@@ -28,6 +28,39 @@
 logger = logging.getLogger(__name__)
 
 
+def _filter_raw_unspecified_fields(headers: NDArray) -> NDArray:
+    """Filter out __MDIO_RAW_UNSPECIFIED_Field_* fields from headers array.
+    
+    These fields are added during SEGY import to preserve raw header bytes,
+    but they cause dtype mismatches during export. This function removes them.
+    
+    Args:
+        headers: Header array that may contain raw unspecified fields.
+        
+    Returns:
+        Header array with raw unspecified fields removed.
+    """
+    if headers.dtype.names is None:
+        return headers
+        
+    # Find field names that don't start with __MDIO_RAW_UNSPECIFIED_
+    field_names = [name for name in headers.dtype.names 
+                   if not name.startswith("__MDIO_RAW_UNSPECIFIED_")]
+    
+    if len(field_names) == len(headers.dtype.names):
+        # No raw unspecified fields found, return as-is
+        return headers
+    
+    # Create new structured array with only the non-raw fields
+    new_dtype = [(name, headers.dtype.fields[name][0]) for name in field_names]
+    filtered_headers = np.empty(headers.shape, dtype=new_dtype)
+    
+    for name in field_names:
+        filtered_headers[name] = headers[name]
+        
+    return filtered_headers
+
+
 def make_segy_factory(spec: SegySpec, binary_header: dict[str, int]) -> SegyFactory:
     """Generate SEG-Y factory from MDIO metadata."""
     sample_interval = binary_header["sample_interval"]
@@ -167,7 +200,9 @@ def serialize_to_segy_stack(  # noqa: PLR0913
         samples = samples[live_mask]
         headers = headers[live_mask]
 
-        buffer = segy_factory.create_traces(headers, samples)
+        # Filter out raw unspecified fields that cause dtype mismatches
+        filtered_headers = _filter_raw_unspecified_fields(headers)
+        buffer = segy_factory.create_traces(filtered_headers, samples)
 
         global_index = block_start[0]
         record_id_str = str(global_index)
@@ -199,7 +234,9 @@ def serialize_to_segy_stack(  # noqa: PLR0913
             rec_samples = samples[rec_index][rec_live_mask]
             rec_headers = headers[rec_index][rec_live_mask]
 
-            buffer = segy_factory.create_traces(rec_headers, rec_samples)
+            # Filter out raw unspecified fields that cause dtype mismatches
+            filtered_headers = _filter_raw_unspecified_fields(rec_headers)
+            buffer = segy_factory.create_traces(filtered_headers, rec_samples)
 
             global_index = tuple(block_start[i] + rec_index[i] for i in range(record_ndim))
             record_id_str = "/".join(map(str, global_index))

From 7d1508e0d8845e8ecf156343c1431b03e50d07b1 Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Wed, 24 Sep 2025 18:31:32 +0000
Subject: [PATCH 14/24] linting pass 1

---
 disaster_recovery_analysis/bootstrap.sh       |  2 +-
 .../ingest_both_teapots.py                    | 14 ++--
 disaster_recovery_analysis/src/main.rs        | 60 ++++++++--------
 src/mdio/converters/segy.py                   | 48 ++++---------
 src/mdio/segy/_disaster_recovery_wrapper.py   | 11 ++-
 src/mdio/segy/_workers.py                     |  2 +-
 src/mdio/segy/creation.py                     | 19 +++--
 .../test_segy_import_export_masked.py         | 70 +++++++++++--------
 tests/unit/test_disaster_recovery_wrapper.py  | 23 ++----
 9 files changed, 114 insertions(+), 135 deletions(-)

diff --git a/disaster_recovery_analysis/bootstrap.sh b/disaster_recovery_analysis/bootstrap.sh
index a6557a2bf..cd5c8d853 100755
--- a/disaster_recovery_analysis/bootstrap.sh
+++ b/disaster_recovery_analysis/bootstrap.sh
@@ -59,7 +59,7 @@ if [ $# -eq 1 ]; then
     ZARR_PATH="$1"
     echo "=== Running hexdump on provided path: $ZARR_PATH ==="
     echo
-    
+
     if [ -e "$ZARR_PATH" ]; then
         ./target/release/zarr-hexdump "$ZARR_PATH"
     else
diff --git a/disaster_recovery_analysis/ingest_both_teapots.py b/disaster_recovery_analysis/ingest_both_teapots.py
index 04aa52f56..fa923a871 100644
--- a/disaster_recovery_analysis/ingest_both_teapots.py
+++ b/disaster_recovery_analysis/ingest_both_teapots.py
@@ -1,11 +1,13 @@
 if __name__ == "__main__":
-    import mdio
-    from segy.standards import get_segy_standard
-    from segy.schema import HeaderField, Endianness
+    import logging
     import os
-    from mdio.builder.template_registry import TemplateRegistry
 
-    import logging
+    from segy.schema import Endianness
+    from segy.schema import HeaderField
+    from segy.standards import get_segy_standard
+
+    import mdio
+    from mdio.builder.template_registry import TemplateRegistry
 
     logging.getLogger("segy").setLevel(logging.DEBUG)
 
@@ -40,4 +42,4 @@
         input_path="filt_mig_IEEE_LittleEndian_Rev1.sgy",
         output_path="filt_mig_IEEE_LittleEndian_Rev1.mdio",
         overwrite=True,
-    )
\ No newline at end of file
+    )
diff --git a/disaster_recovery_analysis/src/main.rs b/disaster_recovery_analysis/src/main.rs
index 974e38089..9cbbffb8b 100644
--- a/disaster_recovery_analysis/src/main.rs
+++ b/disaster_recovery_analysis/src/main.rs
@@ -8,32 +8,32 @@ fn decompress_blosc(compressed_data: &[u8]) -> Result<Vec<u8>, String> {
         let mut nbytes = 0usize;
         let mut cbytes = 0usize;
         let mut blocksize = 0usize;
-        
+
         blosc_sys::blosc_cbuffer_sizes(
             compressed_data.as_ptr() as *const std::ffi::c_void,
             &mut nbytes as *mut usize,
             &mut cbytes as *mut usize,
             &mut blocksize as *mut usize,
         );
-        
+
         if nbytes == 0 {
             return Err("Invalid compressed data".to_string());
         }
-        
+
         // Allocate output buffer
         let mut decompressed = vec![0u8; nbytes];
-        
+
         // Decompress
         let result = blosc_sys::blosc_decompress(
             compressed_data.as_ptr() as *const std::ffi::c_void,
             decompressed.as_mut_ptr() as *mut std::ffi::c_void,
             nbytes,
         );
-        
+
         if result < 0 {
             return Err(format!("Blosc decompression failed with code: {}", result));
         }
-        
+
         decompressed.truncate(result as usize);
         Ok(decompressed)
     }
@@ -43,10 +43,10 @@ fn print_hexdump(data: &[u8], offset: usize, chunk_name: &str) {
     println!("=== {} ===", chunk_name);
     for (i, chunk) in data.chunks(16).enumerate() {
         let addr = offset + i * 16;
-        
+
         // Print address
         print!("{:08x}  ", addr);
-        
+
         // Print hex bytes
         for (j, &byte) in chunk.iter().enumerate() {
             if j == 8 {
@@ -54,7 +54,7 @@ fn print_hexdump(data: &[u8], offset: usize, chunk_name: &str) {
             }
             print!("{:02x} ", byte);
         }
-        
+
         // Pad if chunk is less than 16 bytes
         if chunk.len() < 16 {
             for j in chunk.len()..16 {
@@ -64,7 +64,7 @@ fn print_hexdump(data: &[u8], offset: usize, chunk_name: &str) {
                 print!("   ");
             }
         }
-        
+
         // Print ASCII representation
         print!(" |");
         for &byte in chunk {
@@ -81,38 +81,38 @@ fn print_hexdump(data: &[u8], offset: usize, chunk_name: &str) {
 
 fn main() -> Result<(), Box<dyn std::error::Error>> {
     let args: Vec<String> = env::args().collect();
-    
+
     if args.len() != 2 {
         eprintln!("Usage: {} <zarr_array_path>", args[0]);
         eprintln!("Example: {} /path/to/zarr/array", args[0]);
         std::process::exit(1);
     }
-    
+
     let zarr_path = Path::new(&args[1]);
-    
+
     // Verify the path exists
     if !zarr_path.exists() {
         eprintln!("Error: Path '{}' does not exist", zarr_path.display());
         std::process::exit(1);
     }
-    
+
     println!("Reading Zarr array from: {}", zarr_path.display());
     println!("========================================");
-    
+
     // Read zarr.json metadata
     let zarr_json_path = zarr_path.join("zarr.json");
     if !zarr_json_path.exists() {
         eprintln!("Error: zarr.json not found in {}", zarr_path.display());
         std::process::exit(1);
     }
-    
+
     let metadata_content = fs::read_to_string(&zarr_json_path)?;
     let metadata: serde_json::Value = serde_json::from_str(&metadata_content)?;
-    
+
     // Extract information from metadata
     let shape = metadata["shape"].as_array().unwrap();
     let chunk_shape = metadata["chunk_grid"]["configuration"]["chunk_shape"].as_array().unwrap();
-    
+
     println!("Array shape: {:?}", shape);
     println!("Chunk shape: {:?}", chunk_shape);
     println!("Data type: {}", metadata["data_type"]["name"]);
@@ -122,42 +122,42 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
         }
     }
     println!();
-    
+
     // Calculate expected chunks based on the metadata we know:
     // Shape: [345, 188], Chunk shape: [128, 128]
     // This means we have ceil(345/128) = 3 chunks in dimension 0
     // and ceil(188/128) = 2 chunks in dimension 1
     // So we expect chunks: c/0/0, c/0/1, c/1/0, c/1/1, c/2/0, c/2/1
-    
+
     let mut chunk_files = Vec::new();
-    
+
     // Find all chunk files by walking the directory
     for entry in WalkDir::new(zarr_path) {
         let entry = entry?;
         let path = entry.path();
-        
+
         // Look for chunk files (they start with 'c/' in Zarr v3)
         if path.is_file() {
             let relative_path = path.strip_prefix(zarr_path)?;
             let path_str = relative_path.to_string_lossy();
-            
+
             if path_str.starts_with("c/") {
                 chunk_files.push((path.to_path_buf(), path_str.to_string()));
             }
         }
     }
-    
+
     // Sort chunk files for consistent ordering
     chunk_files.sort_by(|a, b| a.1.cmp(&b.1));
-    
+
     println!("Found {} chunk files:", chunk_files.len());
     for (_, chunk_name) in &chunk_files {
         println!("  {}", chunk_name);
     }
     println!();
-    
+
     let mut total_offset = 0;
-    
+
     // Read, decompress, and hexdump each chunk file
     for (chunk_path, chunk_name) in chunk_files {
         match fs::read(&chunk_path) {
@@ -168,7 +168,7 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
                     println!();
                 } else {
                     println!("Compressed size: {} bytes", compressed_data.len());
-                    
+
                     // Decompress the Blosc-compressed data using blosc-sys directly
                     match decompress_blosc(&compressed_data) {
                         Ok(decompressed_data) => {
@@ -190,11 +190,11 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
             }
         }
     }
-    
+
     println!("Total decompressed bytes processed: {}", total_offset);
     println!();
     println!("Note: This shows the decompressed array data as it would appear in memory.");
     println!("Each element is 240 bytes (raw_bytes with length_bytes: 240).");
-    
+
     Ok(())
 }
diff --git a/src/mdio/converters/segy.py b/src/mdio/converters/segy.py
index 50e020127..22ea6325a 100644
--- a/src/mdio/converters/segy.py
+++ b/src/mdio/converters/segy.py
@@ -4,16 +4,17 @@
 
 import logging
 import os
+from copy import deepcopy
 from typing import TYPE_CHECKING
 
 import numpy as np
 import zarr
 from segy import SegyFile
 from segy.config import SegySettings
-from segy.standards.codes import MeasurementSystem as segy_MeasurementSystem
-from segy.standards.fields.trace import Rev0 as TraceHeaderFieldsRev0
 from segy.schema import HeaderField
 from segy.schema import ScalarType as ScalarType2
+from segy.standards.codes import MeasurementSystem as segy_MeasurementSystem
+from segy.standards.fields.trace import Rev0 as TraceHeaderFieldsRev0
 
 from mdio.api.io import _normalize_path
 from mdio.api.io import to_mdio
@@ -342,48 +343,29 @@ def _add_grid_override_to_metadata(dataset: Dataset, grid_overrides: dict[str, A
     if grid_overrides is not None:
         dataset.metadata.attributes["gridOverrides"] = grid_overrides
 
+
 def _scalar_to_size(scalar: ScalarType2) -> int:
-    if scalar == ScalarType2.UINT8:
-        return 1
-    elif scalar == ScalarType2.UINT16:
-        return 2
-    elif scalar == ScalarType2.UINT32:
-        return 4
-    elif scalar == ScalarType2.UINT64:
+    if scalar == ScalarType2.STRING8:
         return 8
-    elif scalar == ScalarType2.INT8:
-        return 1
-    elif scalar == ScalarType2.INT16:
-        return 2
-    elif scalar == ScalarType2.INT32:
-        return 4
-    elif scalar == ScalarType2.INT64:
-        return 8
-    elif scalar == ScalarType2.FLOAT32:
-        return 4
-    elif scalar == ScalarType2.FLOAT64:
-        return 8
-    elif scalar == ScalarType2.FLOAT16:
-        return 2
-    elif scalar == ScalarType2.STRING8:
-        return 8
-    else:
-        raise ValueError(f"Invalid scalar type: {scalar}")
+
+    return str(scalar).split(".")[1] % 8
+
 
 def _customize_segy_spec(segy_spec: SegySpec) -> SegySpec:
-    from copy import deepcopy
     assigned_bytes = []
 
     ret = deepcopy(segy_spec)
 
     for field in segy_spec.trace.header.fields:
-        byte = field.byte-1
+        byte = field.byte - 1
         for i in range(byte, byte + _scalar_to_size(field.format)):
-            assigned_bytes.append(i)
+            assigned_bytes.append(i)  # noqa: PERF402
     unassigned_bytes = [i for i in range(240) if i not in assigned_bytes]
-    field_to_customize = [HeaderField(name=f"__MDIO_RAW_UNSPECIFIED_Field_{i}", format=ScalarType.UINT8, byte=i+1) for i in unassigned_bytes]
-    ret = ret.customize(trace_header_fields=field_to_customize)
-    return ret
+    field_to_customize = [
+        HeaderField(name=f"__MDIO_RAW_UNSPECIFIED_Field_{i}", format=ScalarType.UINT8, byte=i + 1)
+        for i in unassigned_bytes
+    ]
+    return ret.customize(trace_header_fields=field_to_customize)
 
 
 def _add_raw_headers_to_template(mdio_template: AbstractDatasetTemplate) -> AbstractDatasetTemplate:
diff --git a/src/mdio/segy/_disaster_recovery_wrapper.py b/src/mdio/segy/_disaster_recovery_wrapper.py
index 8b4afb46f..aaa647731 100644
--- a/src/mdio/segy/_disaster_recovery_wrapper.py
+++ b/src/mdio/segy/_disaster_recovery_wrapper.py
@@ -2,17 +2,17 @@
 
 from __future__ import annotations
 
+from copy import deepcopy
 from typing import TYPE_CHECKING
 
-from copy import deepcopy
 import numpy as np
 
 if TYPE_CHECKING:
     from numpy.typing import NDArray
     from segy import SegyFile
 
-class SegyFileTraceDataWrapper:
 
+class SegyFileTraceDataWrapper:
     def __init__(self, segy_file: SegyFile, indices: int | list[int] | NDArray | slice):
         self.segy_file = segy_file
         self.indices = indices
@@ -21,15 +21,14 @@ def __init__(self, segy_file: SegyFile, indices: int | list[int] | NDArray | sli
         self.traces = segy_file.trace[indices]
 
     @property
-    def header(self):
+    def header(self) -> NDArray:
         # The copy is necessary to avoid applying the pipeline to the original header.
         return self._header_pipeline.apply(self.traces.header.copy())
 
-
     @property
-    def raw_header(self):
+    def raw_header(self) -> NDArray:
         return np.ascontiguousarray(self.traces.header.copy()).view("|V240")
 
     @property
-    def sample(self):
+    def sample(self) -> NDArray:
         return self.traces.sample
diff --git a/src/mdio/segy/_workers.py b/src/mdio/segy/_workers.py
index 6ec17d7df..f960811e1 100644
--- a/src/mdio/segy/_workers.py
+++ b/src/mdio/segy/_workers.py
@@ -12,7 +12,6 @@
 
 from mdio.api.io import to_mdio
 from mdio.builder.schemas.dtype import ScalarType
-from mdio.segy._disaster_recovery_wrapper import SegyFileTraceDataWrapper
 
 if TYPE_CHECKING:
     from segy.arrays import HeaderArray
@@ -141,6 +140,7 @@ def trace_worker(  # noqa: PLR0913
     # NOTE: The `raw_header_key` code block should be removed in full as it will become dead code.
     # traces = SegyFileTraceDataWrapper(segy_file, live_trace_indexes)
     from copy import deepcopy
+
     header_pipeline = deepcopy(segy_file.accessors.header_decode_pipeline)
     segy_file.accessors.header_decode_pipeline.transforms = []
     traces = segy_file.trace[live_trace_indexes]
diff --git a/src/mdio/segy/creation.py b/src/mdio/segy/creation.py
index 81cfd13ae..4c5e25a98 100644
--- a/src/mdio/segy/creation.py
+++ b/src/mdio/segy/creation.py
@@ -30,34 +30,33 @@
 
 def _filter_raw_unspecified_fields(headers: NDArray) -> NDArray:
     """Filter out __MDIO_RAW_UNSPECIFIED_Field_* fields from headers array.
-    
+
     These fields are added during SEGY import to preserve raw header bytes,
     but they cause dtype mismatches during export. This function removes them.
-    
+
     Args:
         headers: Header array that may contain raw unspecified fields.
-        
+
     Returns:
         Header array with raw unspecified fields removed.
     """
     if headers.dtype.names is None:
         return headers
-        
+
     # Find field names that don't start with __MDIO_RAW_UNSPECIFIED_
-    field_names = [name for name in headers.dtype.names 
-                   if not name.startswith("__MDIO_RAW_UNSPECIFIED_")]
-    
+    field_names = [name for name in headers.dtype.names if not name.startswith("__MDIO_RAW_UNSPECIFIED_")]
+
     if len(field_names) == len(headers.dtype.names):
         # No raw unspecified fields found, return as-is
         return headers
-    
+
     # Create new structured array with only the non-raw fields
     new_dtype = [(name, headers.dtype.fields[name][0]) for name in field_names]
     filtered_headers = np.empty(headers.shape, dtype=new_dtype)
-    
+
     for name in field_names:
         filtered_headers[name] = headers[name]
-        
+
     return filtered_headers
 
 
diff --git a/tests/integration/test_segy_import_export_masked.py b/tests/integration/test_segy_import_export_masked.py
index 3e96e8a63..71be5e65f 100644
--- a/tests/integration/test_segy_import_export_masked.py
+++ b/tests/integration/test_segy_import_export_masked.py
@@ -288,7 +288,7 @@ def export_masked_path(tmp_path_factory: pytest.TempPathFactory, raw_headers_env
     # raw_headers_env dependency ensures the environment variable is set before this runs
     raw_headers_enabled = os.getenv("MDIO__DO_RAW_HEADERS") == "1"
     path_suffix = "with_raw_headers" if raw_headers_enabled else "without_raw_headers"
-    
+
     if DEBUG_MODE:
         return Path(f"TMP/export_masked_{path_suffix}")
     return tmp_path_factory.getbasetemp() / f"export_masked_{path_suffix}"
@@ -307,16 +307,23 @@ def raw_headers_env(request: pytest.FixtureRequest) -> None:
 
     # Cleanup after test - both environment variable and template state
     os.environ.pop("MDIO__DO_RAW_HEADERS", None)
-    
+
     # Clean up any template modifications to ensure test isolation
     from mdio.builder.template_registry import TemplateRegistry
+
     registry = TemplateRegistry.get_instance()
-    
+
     # Reset any templates that might have been modified with raw headers
-    template_names = ["PostStack2DTime", "PostStack3DTime", "PreStackCdpOffsetGathers2DTime", 
-                     "PreStackCdpOffsetGathers3DTime", "PreStackShotGathers2DTime", 
-                     "PreStackShotGathers3DTime", "PreStackCocaGathers3DTime"]
-    
+    template_names = [
+        "PostStack2DTime",
+        "PostStack3DTime",
+        "PreStackCdpOffsetGathers2DTime",
+        "PreStackCdpOffsetGathers3DTime",
+        "PreStackShotGathers2DTime",
+        "PreStackShotGathers3DTime",
+        "PreStackCocaGathers3DTime",
+    ]
+
     for template_name in template_names:
         try:
             template = registry.get(template_name)
@@ -327,7 +334,7 @@ def raw_headers_env(request: pytest.FixtureRequest) -> None:
                 # We need to restore it to the original method from the class
                 # Since we can't easily restore the exact original, we'll get a fresh instance
                 template_class = type(template)
-                if hasattr(template_class, '_add_variables'):
+                if hasattr(template_class, "_add_variables"):
                     template._add_variables = template_class._add_variables.__get__(template, template_class)
         except KeyError:
             # Template not found, skip
@@ -523,18 +530,20 @@ def test_raw_headers_byte_preservation(
         else:
             assert not has_raw_headers, f"raw_headers should not be present when MDIO__DO_RAW_HEADERS is not set\n {ds}"
             return  # Exit early if raw_headers are not expected
-        
+
         # Get data (only if raw_headers exist)
         raw_headers_data = ds.raw_headers.values
         trace_mask = ds.trace_mask.values
-        
+
         # Verify 240-byte headers
-        assert raw_headers_data.dtype.itemsize == 240, f"Expected 240-byte headers, got {raw_headers_data.dtype.itemsize}"
-        
+        assert raw_headers_data.dtype.itemsize == 240, (
+            f"Expected 240-byte headers, got {raw_headers_data.dtype.itemsize}"
+        )
+
         # Read raw bytes directly from SEG-Y file
         def read_segy_trace_header(trace_index: int) -> bytes:
             """Read 240-byte trace header directly from SEG-Y file."""
-            with open(segy_path, 'rb') as f:
+            with open(segy_path, "rb") as f:
                 # Skip text (3200) + binary (400) headers = 3600 bytes
                 f.seek(3600)
                 # Each trace: 240 byte header + (num_samples * 4) byte samples
@@ -542,41 +551,41 @@ def read_segy_trace_header(trace_index: int) -> bytes:
                 trace_offset = trace_index * trace_size
                 f.seek(trace_offset, 1)  # Seek relative to current position
                 return f.read(240)
-        
+
         # Compare all valid traces byte-by-byte
         segy_trace_idx = 0
         flat_mask = trace_mask.ravel()
         flat_raw_headers = raw_headers_data.ravel()  # Flatten to 1D array of 240-byte header records
 
-        operation = 'w'
-        
+        operation = "w"
+
         for grid_idx in range(flat_mask.size):
             if not flat_mask[grid_idx]:
                 print(f"Skipping trace {grid_idx} because it is masked")
                 continue
-                
+
             # Get MDIO header as bytes - convert single header record to bytes
             header_record = flat_raw_headers[grid_idx]
             mdio_header_bytes = np.frombuffer(header_record.tobytes(), dtype=np.uint8)
-            
+
             # Get SEG-Y header as raw bytes directly from file
             segy_raw_header_bytes = read_segy_trace_header(segy_trace_idx)
             segy_header_bytes = np.frombuffer(segy_raw_header_bytes, dtype=np.uint8)
 
             assert_array_equal(mdio_header_bytes, segy_header_bytes)
-            
+
             # Compare byte-by-byte
             # Write hexdumps to separate files for analysis
             # def hexdump_to_string(data: bytes, title: str) -> str:
             #     """Create hexdump string."""
             #     lines = [f"{title}", "=" * len(title), ""]
-                 
+
             #     for i in range(0, len(data), 16):
             #         # Address
             #         addr = i
             #         hex_part = ""
             #         ascii_part = ""
-                     
+
             #         # Process 16 bytes at a time
             #         for j in range(16):
             #             if i + j < len(data):
@@ -586,25 +595,25 @@ def read_segy_trace_header(trace_index: int) -> bytes:
             #             else:
             #                 hex_part += "   "
             #                 ascii_part += " "
-                     
+
             #         lines.append(f"{addr:08x}: {hex_part} |{ascii_part}|")
-                 
+
             #     return "\n".join(lines)
-             
+
             # # Generate filenames for this test case
             # segy_filename = f"segy_headers_{grid_conf.name}.txt"
             # mdio_filename = f"mdio_headers_{grid_conf.name}.txt"
-             
+
             # # Append SEG-Y hexdump to file
             # with open(segy_filename, operation) as f:
             #     if segy_trace_idx == 0:
             #         f.write("")  # Start fresh for first trace
             #     else:
             #         f.write("\n\n")  # Add spacing between traces
-            #     f.write(hexdump_to_string(segy_header_bytes, 
+            #     f.write(hexdump_to_string(segy_header_bytes,
             #                             f"SEG-Y Header - {grid_conf.name} Trace {segy_trace_idx} (240 bytes)"))
-             
-            # # Append MDIO hexdump to file  
+
+            # # Append MDIO hexdump to file
             # with open(mdio_filename, operation) as f:
             #     if segy_trace_idx == 0:
             #         f.write("")  # Start fresh for first trace
@@ -613,11 +622,10 @@ def read_segy_trace_header(trace_index: int) -> bytes:
             #     f.write(hexdump_to_string(mdio_header_bytes,
             #                             f"MDIO Raw Header - {grid_conf.name} Trace {segy_trace_idx} (240 bytes)"))
             # operation = 'a'
-             
+
             # if segy_trace_idx == 0:
             #     print(f"\nHeader hexdumps being written for {grid_conf.name}:")
             #     print(f"  SEG-Y: {segy_filename}")
             #     print(f"  MDIO:  {mdio_filename}")
-                
-            
+
             segy_trace_idx += 1
diff --git a/tests/unit/test_disaster_recovery_wrapper.py b/tests/unit/test_disaster_recovery_wrapper.py
index e4e3e31fa..bb1864f67 100644
--- a/tests/unit/test_disaster_recovery_wrapper.py
+++ b/tests/unit/test_disaster_recovery_wrapper.py
@@ -9,7 +9,6 @@
 
 import tempfile
 from pathlib import Path
-from typing import TYPE_CHECKING
 
 import numpy as np
 import pytest
@@ -22,9 +21,6 @@
 
 from mdio.segy._disaster_recovery_wrapper import SegyFileTraceDataWrapper
 
-if TYPE_CHECKING:
-    from numpy.typing import NDArray
-
 SAMPLES_PER_TRACE = 1501
 
 
@@ -118,10 +114,7 @@ def create_test_segy_file(  # noqa: PLR0913
 
         return spec
 
-
-    def test_wrapper_basic_functionality(
-        self, temp_dir: Path, basic_segy_spec: SegySpec, segy_config: dict
-    ) -> None:
+    def test_wrapper_basic_functionality(self, temp_dir: Path, basic_segy_spec: SegySpec, segy_config: dict) -> None:
         """Test basic functionality of SegyFileTraceDataWrapper."""
         config_name = segy_config["name"]
         endianness = segy_config["endianness"]
@@ -160,14 +153,12 @@ def test_wrapper_basic_functionality(
 
         # Raw header should be bytes (240 bytes per trace header)
         assert raw_header.dtype == np.dtype("|V240")
-        
+
         # Transformed header should have the expected fields
         assert "inline" in transformed_header.dtype.names
         assert "crossline" in transformed_header.dtype.names
 
-    def test_wrapper_with_multiple_traces(
-        self, temp_dir: Path, basic_segy_spec: SegySpec, segy_config: dict
-    ) -> None:
+    def test_wrapper_with_multiple_traces(self, temp_dir: Path, basic_segy_spec: SegySpec, segy_config: dict) -> None:
         """Test wrapper with multiple traces."""
         config_name = segy_config["name"]
         endianness = segy_config["endianness"]
@@ -297,9 +288,7 @@ def test_different_index_types(
 
         assert wrapper.header.size == expected_count
 
-    def test_header_pipeline_preservation(
-        self, temp_dir: Path, basic_segy_spec: SegySpec, segy_config: dict
-    ) -> None:
+    def test_header_pipeline_preservation(self, temp_dir: Path, basic_segy_spec: SegySpec, segy_config: dict) -> None:
         """Test that the wrapper preserves the original header pipeline."""
         config_name = segy_config["name"]
         endianness = segy_config["endianness"]
@@ -322,7 +311,7 @@ def test_header_pipeline_preservation(
 
         # Load the SEGY file
         segy_file = SegyFile(segy_path, spec=spec)
-        
+
         # Store original pipeline transforms count
         original_transforms_count = len(segy_file.accessors.header_decode_pipeline.transforms)
 
@@ -331,6 +320,6 @@ def test_header_pipeline_preservation(
 
         # Verify that the original SEGY file's pipeline was modified (transforms cleared)
         assert len(segy_file.accessors.header_decode_pipeline.transforms) == 0
-        
+
         # Verify that the wrapper has its own pipeline with the original transforms
         assert len(wrapper._header_pipeline.transforms) == original_transforms_count

From 743104fb4d7b0f1dbf754b0426a8d8a810cce05e Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Wed, 24 Sep 2025 19:11:39 +0000
Subject: [PATCH 15/24] Fix logic issue

---
 src/mdio/converters/segy.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/mdio/converters/segy.py b/src/mdio/converters/segy.py
index 22ea6325a..d5403b9c2 100644
--- a/src/mdio/converters/segy.py
+++ b/src/mdio/converters/segy.py
@@ -345,10 +345,13 @@ def _add_grid_override_to_metadata(dataset: Dataset, grid_overrides: dict[str, A
 
 
 def _scalar_to_size(scalar: ScalarType2) -> int:
+    # TODO(BrianMichell): #0000 Lazy way to support conversion.
     if scalar == ScalarType2.STRING8:
         return 8
-
-    return str(scalar).split(".")[1] % 8
+    try:
+        return int(str(scalar)[-2:]) // 8
+    except ValueError:
+        return 1
 
 
 def _customize_segy_spec(segy_spec: SegySpec) -> SegySpec:

From b3cb37ae9def23e5807cc72d5b36339e8eed33fb Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Wed, 24 Sep 2025 19:15:24 +0000
Subject: [PATCH 16/24] Use wrapper class

---
 src/mdio/segy/_workers.py | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/src/mdio/segy/_workers.py b/src/mdio/segy/_workers.py
index f960811e1..184aa488a 100644
--- a/src/mdio/segy/_workers.py
+++ b/src/mdio/segy/_workers.py
@@ -12,6 +12,7 @@
 
 from mdio.api.io import to_mdio
 from mdio.builder.schemas.dtype import ScalarType
+from mdio.segy._disaster_recovery_wrapper import SegyFileTraceDataWrapper
 
 if TYPE_CHECKING:
     from segy.arrays import HeaderArray
@@ -138,18 +139,13 @@ def trace_worker(  # noqa: PLR0913
     # For that reason, we have wrapped the accessors to provide an interface that can be removed
     # and not require additional changes to the below code.
     # NOTE: The `raw_header_key` code block should be removed in full as it will become dead code.
-    # traces = SegyFileTraceDataWrapper(segy_file, live_trace_indexes)
-    from copy import deepcopy
-
-    header_pipeline = deepcopy(segy_file.accessors.header_decode_pipeline)
-    segy_file.accessors.header_decode_pipeline.transforms = []
-    traces = segy_file.trace[live_trace_indexes]
+    traces = SegyFileTraceDataWrapper(segy_file, live_trace_indexes)
 
     ds_to_write = dataset[worker_variables]
 
     if raw_header_key in worker_variables:
         tmp_raw_headers = np.zeros_like(dataset[raw_header_key])
-        tmp_raw_headers[not_null] = np.ascontiguousarray(traces.header.copy()).view("|V240")
+        tmp_raw_headers[not_null] = traces.raw_header
 
         ds_to_write[raw_header_key] = Variable(
             ds_to_write[raw_header_key].dims,
@@ -162,8 +158,7 @@ def trace_worker(  # noqa: PLR0913
         # TODO(BrianMichell): Implement this better so that we can enable fill values without changing the code
         # https://github.com/TGSAI/mdio-python/issues/584
         tmp_headers = np.zeros_like(dataset[header_key])
-        # tmp_headers[not_null] = traces.header
-        tmp_headers[not_null] = header_pipeline.apply(traces.header.copy())
+        tmp_headers[not_null] = traces.header
         # Create a new Variable object to avoid copying the temporary array
         # The ideal solution is to use `ds_to_write[header_key][:] = tmp_headers`
         # but Xarray appears to be copying memory instead of doing direct assignment.

From 2330e8f9d68a313cb4bb8058692e33b59a6757e4 Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Wed, 24 Sep 2025 19:19:18 +0000
Subject: [PATCH 17/24] Precommit

---
 tests/integration/test_segy_import_export_masked.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/tests/integration/test_segy_import_export_masked.py b/tests/integration/test_segy_import_export_masked.py
index 71be5e65f..023544b1b 100644
--- a/tests/integration/test_segy_import_export_masked.py
+++ b/tests/integration/test_segy_import_export_masked.py
@@ -309,8 +309,6 @@ def raw_headers_env(request: pytest.FixtureRequest) -> None:
     os.environ.pop("MDIO__DO_RAW_HEADERS", None)
 
     # Clean up any template modifications to ensure test isolation
-    from mdio.builder.template_registry import TemplateRegistry
-
     registry = TemplateRegistry.get_instance()
 
     # Reset any templates that might have been modified with raw headers
@@ -543,7 +541,8 @@ def test_raw_headers_byte_preservation(
         # Read raw bytes directly from SEG-Y file
         def read_segy_trace_header(trace_index: int) -> bytes:
             """Read 240-byte trace header directly from SEG-Y file."""
-            with open(segy_path, "rb") as f:
+            # with open(segy_path, "rb") as f:
+            with Path.open(segy_path, "rb") as f:
                 # Skip text (3200) + binary (400) headers = 3600 bytes
                 f.seek(3600)
                 # Each trace: 240 byte header + (num_samples * 4) byte samples
@@ -557,7 +556,7 @@ def read_segy_trace_header(trace_index: int) -> bytes:
         flat_mask = trace_mask.ravel()
         flat_raw_headers = raw_headers_data.ravel()  # Flatten to 1D array of 240-byte header records
 
-        operation = "w"
+        # operation = "w"
 
         for grid_idx in range(flat_mask.size):
             if not flat_mask[grid_idx]:

From 6d9159cbbc4b19c6bbe5674e9f28d16d505a4e03 Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Wed, 24 Sep 2025 19:20:19 +0000
Subject: [PATCH 18/24] Remove external debugging code

---
 disaster_recovery_analysis/bootstrap.sh       |  76 -------
 .../ingest_both_teapots.py                    |  45 ----
 disaster_recovery_analysis/src/main.rs        | 200 ------------------
 3 files changed, 321 deletions(-)
 delete mode 100755 disaster_recovery_analysis/bootstrap.sh
 delete mode 100644 disaster_recovery_analysis/ingest_both_teapots.py
 delete mode 100644 disaster_recovery_analysis/src/main.rs

diff --git a/disaster_recovery_analysis/bootstrap.sh b/disaster_recovery_analysis/bootstrap.sh
deleted file mode 100755
index cd5c8d853..000000000
--- a/disaster_recovery_analysis/bootstrap.sh
+++ /dev/null
@@ -1,76 +0,0 @@
-#!/bin/bash
-
-set -e  # Exit on any error
-
-echo "=== Zarr Hexdump Bootstrap Script ==="
-echo
-
-# Check if Rust is installed, if not install it
-if ! command -v rustc &> /dev/null; then
-    echo "Rust is not installed. Installing Rust..."
-    curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
-    source $HOME/.cargo/env
-    echo "✓ Rust installed successfully"
-fi
-
-echo "✓ Rust is installed ($(rustc --version))"
-
-# Check if Cargo is available
-if ! command -v cargo &> /dev/null; then
-    echo "Sourcing Rust environment..."
-    source $HOME/.cargo/env
-fi
-
-echo "✓ Cargo is available ($(cargo --version))"
-echo
-
-# Install blosc library if not present
-echo "Checking for blosc library..."
-if ! pkg-config --exists blosc; then
-    echo "Installing blosc library..."
-    sudo apt-get update
-    sudo apt-get install -y libblosc-dev pkg-config
-    echo "✓ Blosc library installed"
-else
-    echo "✓ Blosc library already available"
-fi
-echo
-
-# Build the project
-echo "Building the Zarr hexdump tool..."
-if cargo build --release; then
-    echo "✓ Build successful!"
-else
-    echo "✗ Build failed!"
-    exit 1
-fi
-
-echo
-echo "=== Usage ==="
-echo "To hexdump a Zarr array, run:"
-echo "  ./target/release/zarr-hexdump /path/to/your/zarr/array"
-echo
-echo "Or use cargo run:"
-echo "  cargo run --release -- /path/to/your/zarr/array"
-echo
-
-# Check if a path was provided as an argument
-if [ $# -eq 1 ]; then
-    ZARR_PATH="$1"
-    echo "=== Running hexdump on provided path: $ZARR_PATH ==="
-    echo
-
-    if [ -e "$ZARR_PATH" ]; then
-        ./target/release/zarr-hexdump "$ZARR_PATH"
-    else
-        echo "Error: Path '$ZARR_PATH' does not exist!"
-        exit 1
-    fi
-elif [ $# -gt 1 ]; then
-    echo "Error: Too many arguments provided."
-    echo "Usage: $0 [zarr_array_path]"
-    exit 1
-else
-    echo "No Zarr array path provided. Build completed successfully."
-    echo "Use the commands above to run the hexdump tool."
-fi
diff --git a/disaster_recovery_analysis/ingest_both_teapots.py b/disaster_recovery_analysis/ingest_both_teapots.py
deleted file mode 100644
index fa923a871..000000000
--- a/disaster_recovery_analysis/ingest_both_teapots.py
+++ /dev/null
@@ -1,45 +0,0 @@
-if __name__ == "__main__":
-    import logging
-    import os
-
-    from segy.schema import Endianness
-    from segy.schema import HeaderField
-    from segy.standards import get_segy_standard
-
-    import mdio
-    from mdio.builder.template_registry import TemplateRegistry
-
-    logging.getLogger("segy").setLevel(logging.DEBUG)
-
-    os.environ["MDIO__IMPORT__CLOUD_NATIVE"] = "true"
-    os.environ["MDIO__IMPORT__CPU_COUNT"] = "16"
-    os.environ["MDIO__DO_RAW_HEADERS"] = "1"
-
-    custom_headers = [
-        HeaderField(name="inline", byte=181, format="int32"),
-        HeaderField(name="crossline", byte=185, format="int32"),
-        HeaderField(name="cdp_x", byte=81, format="int32"),
-        HeaderField(name="cdp_y", byte=85, format="int32"),
-    ]
-
-    big_endian_spec = get_segy_standard(0)
-    big_endian_spec.endianness = Endianness.BIG
-    little_endian_spec = get_segy_standard(0)
-    little_endian_spec.endianness = Endianness.LITTLE
-    big_endian_spec = big_endian_spec.customize(trace_header_fields=custom_headers)
-    little_endian_spec = little_endian_spec.customize(trace_header_fields=custom_headers)
-
-    mdio.segy_to_mdio(
-        segy_spec=big_endian_spec,
-        mdio_template=TemplateRegistry().get("PostStack3DTime"),
-        input_path="filt_mig_IEEE_BigEndian_Rev1.sgy",
-        output_path="filt_mig_IEEE_BigEndian_Rev1.mdio",
-        overwrite=True,
-    )
-    mdio.segy_to_mdio(
-        segy_spec=little_endian_spec,
-        mdio_template=TemplateRegistry().get("PostStack3DTime"),
-        input_path="filt_mig_IEEE_LittleEndian_Rev1.sgy",
-        output_path="filt_mig_IEEE_LittleEndian_Rev1.mdio",
-        overwrite=True,
-    )
diff --git a/disaster_recovery_analysis/src/main.rs b/disaster_recovery_analysis/src/main.rs
deleted file mode 100644
index 9cbbffb8b..000000000
--- a/disaster_recovery_analysis/src/main.rs
+++ /dev/null
@@ -1,200 +0,0 @@
-use std::env;
-use std::fs;
-use std::path::Path;
-use walkdir::WalkDir;
-fn decompress_blosc(compressed_data: &[u8]) -> Result<Vec<u8>, String> {
-    unsafe {
-        // Get decompressed size first
-        let mut nbytes = 0usize;
-        let mut cbytes = 0usize;
-        let mut blocksize = 0usize;
-
-        blosc_sys::blosc_cbuffer_sizes(
-            compressed_data.as_ptr() as *const std::ffi::c_void,
-            &mut nbytes as *mut usize,
-            &mut cbytes as *mut usize,
-            &mut blocksize as *mut usize,
-        );
-
-        if nbytes == 0 {
-            return Err("Invalid compressed data".to_string());
-        }
-
-        // Allocate output buffer
-        let mut decompressed = vec![0u8; nbytes];
-
-        // Decompress
-        let result = blosc_sys::blosc_decompress(
-            compressed_data.as_ptr() as *const std::ffi::c_void,
-            decompressed.as_mut_ptr() as *mut std::ffi::c_void,
-            nbytes,
-        );
-
-        if result < 0 {
-            return Err(format!("Blosc decompression failed with code: {}", result));
-        }
-
-        decompressed.truncate(result as usize);
-        Ok(decompressed)
-    }
-}
-
-fn print_hexdump(data: &[u8], offset: usize, chunk_name: &str) {
-    println!("=== {} ===", chunk_name);
-    for (i, chunk) in data.chunks(16).enumerate() {
-        let addr = offset + i * 16;
-
-        // Print address
-        print!("{:08x}  ", addr);
-
-        // Print hex bytes
-        for (j, &byte) in chunk.iter().enumerate() {
-            if j == 8 {
-                print!(" "); // Extra space in the middle
-            }
-            print!("{:02x} ", byte);
-        }
-
-        // Pad if chunk is less than 16 bytes
-        if chunk.len() < 16 {
-            for j in chunk.len()..16 {
-                if j == 8 {
-                    print!(" ");
-                }
-                print!("   ");
-            }
-        }
-
-        // Print ASCII representation
-        print!(" |");
-        for &byte in chunk {
-            if byte >= 32 && byte <= 126 {
-                print!("{}", byte as char);
-            } else {
-                print!(".");
-            }
-        }
-        println!("|");
-    }
-    println!();
-}
-
-fn main() -> Result<(), Box<dyn std::error::Error>> {
-    let args: Vec<String> = env::args().collect();
-
-    if args.len() != 2 {
-        eprintln!("Usage: {} <zarr_array_path>", args[0]);
-        eprintln!("Example: {} /path/to/zarr/array", args[0]);
-        std::process::exit(1);
-    }
-
-    let zarr_path = Path::new(&args[1]);
-
-    // Verify the path exists
-    if !zarr_path.exists() {
-        eprintln!("Error: Path '{}' does not exist", zarr_path.display());
-        std::process::exit(1);
-    }
-
-    println!("Reading Zarr array from: {}", zarr_path.display());
-    println!("========================================");
-
-    // Read zarr.json metadata
-    let zarr_json_path = zarr_path.join("zarr.json");
-    if !zarr_json_path.exists() {
-        eprintln!("Error: zarr.json not found in {}", zarr_path.display());
-        std::process::exit(1);
-    }
-
-    let metadata_content = fs::read_to_string(&zarr_json_path)?;
-    let metadata: serde_json::Value = serde_json::from_str(&metadata_content)?;
-
-    // Extract information from metadata
-    let shape = metadata["shape"].as_array().unwrap();
-    let chunk_shape = metadata["chunk_grid"]["configuration"]["chunk_shape"].as_array().unwrap();
-
-    println!("Array shape: {:?}", shape);
-    println!("Chunk shape: {:?}", chunk_shape);
-    println!("Data type: {}", metadata["data_type"]["name"]);
-    if let Some(config) = metadata["data_type"]["configuration"].as_object() {
-        if let Some(length_bytes) = config.get("length_bytes") {
-            println!("Length bytes: {}", length_bytes);
-        }
-    }
-    println!();
-
-    // Calculate expected chunks based on the metadata we know:
-    // Shape: [345, 188], Chunk shape: [128, 128]
-    // This means we have ceil(345/128) = 3 chunks in dimension 0
-    // and ceil(188/128) = 2 chunks in dimension 1
-    // So we expect chunks: c/0/0, c/0/1, c/1/0, c/1/1, c/2/0, c/2/1
-
-    let mut chunk_files = Vec::new();
-
-    // Find all chunk files by walking the directory
-    for entry in WalkDir::new(zarr_path) {
-        let entry = entry?;
-        let path = entry.path();
-
-        // Look for chunk files (they start with 'c/' in Zarr v3)
-        if path.is_file() {
-            let relative_path = path.strip_prefix(zarr_path)?;
-            let path_str = relative_path.to_string_lossy();
-
-            if path_str.starts_with("c/") {
-                chunk_files.push((path.to_path_buf(), path_str.to_string()));
-            }
-        }
-    }
-
-    // Sort chunk files for consistent ordering
-    chunk_files.sort_by(|a, b| a.1.cmp(&b.1));
-
-    println!("Found {} chunk files:", chunk_files.len());
-    for (_, chunk_name) in &chunk_files {
-        println!("  {}", chunk_name);
-    }
-    println!();
-
-    let mut total_offset = 0;
-
-    // Read, decompress, and hexdump each chunk file
-    for (chunk_path, chunk_name) in chunk_files {
-        match fs::read(&chunk_path) {
-            Ok(compressed_data) => {
-                if compressed_data.is_empty() {
-                    println!("=== {} ===", chunk_name);
-                    println!("(empty chunk)");
-                    println!();
-                } else {
-                    println!("Compressed size: {} bytes", compressed_data.len());
-
-                    // Decompress the Blosc-compressed data using blosc-sys directly
-                    match decompress_blosc(&compressed_data) {
-                        Ok(decompressed_data) => {
-                            println!("Decompressed size: {} bytes", decompressed_data.len());
-                            print_hexdump(&decompressed_data, total_offset, &chunk_name);
-                            total_offset += decompressed_data.len();
-                        }
-                        Err(e) => {
-                            eprintln!("Error decompressing chunk {}: {}", chunk_name, e);
-                            println!("Showing raw compressed data instead:");
-                            print_hexdump(&compressed_data, total_offset, &format!("{} (compressed)", chunk_name));
-                            total_offset += compressed_data.len();
-                        }
-                    }
-                }
-            }
-            Err(e) => {
-                eprintln!("Error reading chunk {}: {}", chunk_name, e);
-            }
-        }
-    }
-
-    println!("Total decompressed bytes processed: {}", total_offset);
-    println!();
-    println!("Note: This shows the decompressed array data as it would appear in memory.");
-    println!("Each element is 240 bytes (raw_bytes with length_bytes: 240).");
-
-    Ok(())
-}

From e0a1e6a9357dedb67e20d08257b85d1b4b00ae8e Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Wed, 24 Sep 2025 19:27:08 +0000
Subject: [PATCH 19/24] Remove debug code

---
 .../test_segy_import_export_masked.py         | 56 -------------------
 1 file changed, 56 deletions(-)

diff --git a/tests/integration/test_segy_import_export_masked.py b/tests/integration/test_segy_import_export_masked.py
index 023544b1b..fcd0df467 100644
--- a/tests/integration/test_segy_import_export_masked.py
+++ b/tests/integration/test_segy_import_export_masked.py
@@ -556,8 +556,6 @@ def read_segy_trace_header(trace_index: int) -> bytes:
         flat_mask = trace_mask.ravel()
         flat_raw_headers = raw_headers_data.ravel()  # Flatten to 1D array of 240-byte header records
 
-        # operation = "w"
-
         for grid_idx in range(flat_mask.size):
             if not flat_mask[grid_idx]:
                 print(f"Skipping trace {grid_idx} because it is masked")
@@ -573,58 +571,4 @@ def read_segy_trace_header(trace_index: int) -> bytes:
 
             assert_array_equal(mdio_header_bytes, segy_header_bytes)
 
-            # Compare byte-by-byte
-            # Write hexdumps to separate files for analysis
-            # def hexdump_to_string(data: bytes, title: str) -> str:
-            #     """Create hexdump string."""
-            #     lines = [f"{title}", "=" * len(title), ""]
-
-            #     for i in range(0, len(data), 16):
-            #         # Address
-            #         addr = i
-            #         hex_part = ""
-            #         ascii_part = ""
-
-            #         # Process 16 bytes at a time
-            #         for j in range(16):
-            #             if i + j < len(data):
-            #                 byte_val = data[i + j]
-            #                 hex_part += f"{byte_val:02x} "
-            #                 ascii_part += chr(byte_val) if 32 <= byte_val <= 126 else "."
-            #             else:
-            #                 hex_part += "   "
-            #                 ascii_part += " "
-
-            #         lines.append(f"{addr:08x}: {hex_part} |{ascii_part}|")
-
-            #     return "\n".join(lines)
-
-            # # Generate filenames for this test case
-            # segy_filename = f"segy_headers_{grid_conf.name}.txt"
-            # mdio_filename = f"mdio_headers_{grid_conf.name}.txt"
-
-            # # Append SEG-Y hexdump to file
-            # with open(segy_filename, operation) as f:
-            #     if segy_trace_idx == 0:
-            #         f.write("")  # Start fresh for first trace
-            #     else:
-            #         f.write("\n\n")  # Add spacing between traces
-            #     f.write(hexdump_to_string(segy_header_bytes,
-            #                             f"SEG-Y Header - {grid_conf.name} Trace {segy_trace_idx} (240 bytes)"))
-
-            # # Append MDIO hexdump to file
-            # with open(mdio_filename, operation) as f:
-            #     if segy_trace_idx == 0:
-            #         f.write("")  # Start fresh for first trace
-            #     else:
-            #         f.write("\n\n")  # Add spacing between traces
-            #     f.write(hexdump_to_string(mdio_header_bytes,
-            #                             f"MDIO Raw Header - {grid_conf.name} Trace {segy_trace_idx} (240 bytes)"))
-            # operation = 'a'
-
-            # if segy_trace_idx == 0:
-            #     print(f"\nHeader hexdumps being written for {grid_conf.name}:")
-            #     print(f"  SEG-Y: {segy_filename}")
-            #     print(f"  MDIO:  {mdio_filename}")
-
             segy_trace_idx += 1

From 8d5d177720e8c0877465ab49adb76cdd2f743641 Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Wed, 24 Sep 2025 19:39:34 +0000
Subject: [PATCH 20/24] Remove errant numpy additon to pyproject toml

---
 pyproject.toml | 1 -
 uv.lock        | 8 ++++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index afa143a07..4a0dd004b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,7 +22,6 @@ dependencies = [
     "click-params>=0.5.0",
     "dask>=2025.9.0",
     "fsspec>=2025.9.0",
-    "numpy>=2.3.3",
     "pint>=0.25.0",
     "psutil>=7.0.0",
     "pydantic>=2.11.9",
diff --git a/uv.lock b/uv.lock
index d81f73271..4cbcb83e6 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1863,7 +1863,6 @@ dependencies = [
     { name = "click-params" },
     { name = "dask" },
     { name = "fsspec" },
-    { name = "numpy" },
     { name = "pint" },
     { name = "psutil" },
     { name = "pydantic" },
@@ -1926,7 +1925,6 @@ requires-dist = [
     { name = "distributed", marker = "extra == 'distributed'", specifier = ">=2025.9.0" },
     { name = "fsspec", specifier = ">=2025.9.0" },
     { name = "gcsfs", marker = "extra == 'cloud'", specifier = ">=2025.9.0" },
-    { name = "numpy", specifier = ">=2.3.3" },
     { name = "pint", specifier = ">=0.25.0" },
     { name = "psutil", specifier = ">=7.0.0" },
     { name = "pydantic", specifier = ">=2.11.9" },
@@ -3137,26 +3135,32 @@ version = "0.2.14"
 source = { registry = "https://pypi.org/simple" }
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From b9e06e99610fff2185895ddb678f8062934e7078 Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Wed, 24 Sep 2025 19:40:31 +0000
Subject: [PATCH 21/24] Fix uv lock to mainline

---
 uv.lock | 191 ++++++++++++++++++++++++++------------------------------
 1 file changed, 90 insertions(+), 101 deletions(-)

diff --git a/uv.lock b/uv.lock
index 4cbcb83e6..1a745d44d 100644
--- a/uv.lock
+++ b/uv.lock
@@ -573,63 +573,55 @@ wheels = [
 
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+    { url = "https://files.pythonhosted.org/packages/30/8c/ed73f047a73638257aa9377ad356bea4d96125b305c34a28766f4445cc0f/ruamel.yaml.clib-0.2.12-cp313-cp313-win32.whl", hash = "sha256:6442cb36270b3afb1b4951f060eccca1ce49f3d087ca1ca4563a6eb479cb3de6", size = 98583, upload-time = "2024-10-20T10:13:09.658Z" },
+    { url = "https://files.pythonhosted.org/packages/b0/85/e8e751d8791564dd333d5d9a4eab0a7a115f7e349595417fd50ecae3395c/ruamel.yaml.clib-0.2.12-cp313-cp313-win_amd64.whl", hash = "sha256:e5b8daf27af0b90da7bb903a876477a9e6d7270be6146906b276605997c7e9a3", size = 115190, upload-time = "2024-10-20T10:13:10.66Z" },
 ]
 
 [[package]]
@@ -3697,15 +3686,15 @@ wheels = [
 
 [[package]]
 name = "uvicorn"
-version = "0.36.0"
+version = "0.35.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "click" },
     { name = "h11" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/ef/5e/f0cd46063a02fd8515f0e880c37d2657845b7306c16ce6c4ffc44afd9036/uvicorn-0.36.0.tar.gz", hash = "sha256:527dc68d77819919d90a6b267be55f0e76704dca829d34aea9480be831a9b9d9", size = 80032, upload-time = "2025-09-20T01:07:14.418Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/5e/42/e0e305207bb88c6b8d3061399c6a961ffe5fbb7e2aa63c9234df7259e9cd/uvicorn-0.35.0.tar.gz", hash = "sha256:bc662f087f7cf2ce11a1d7fd70b90c9f98ef2e2831556dd078d131b96cc94a01", size = 78473, upload-time = "2025-06-28T16:15:46.058Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/96/06/5cc0542b47c0338c1cb676b348e24a1c29acabc81000bced518231dded6f/uvicorn-0.36.0-py3-none-any.whl", hash = "sha256:6bb4ba67f16024883af8adf13aba3a9919e415358604ce46780d3f9bdc36d731", size = 67675, upload-time = "2025-09-20T01:07:12.984Z" },
+    { url = "https://files.pythonhosted.org/packages/d2/e2/dc81b1bd1dcfe91735810265e9d26bc8ec5da45b4c0f6237e286819194c3/uvicorn-0.35.0-py3-none-any.whl", hash = "sha256:197535216b25ff9b785e29a0b79199f55222193d47f820816e7da751e9bc8d4a", size = 66406, upload-time = "2025-06-28T16:15:44.816Z" },
 ]
 
 [[package]]
@@ -3797,11 +3786,11 @@ wheels = [
 
 [[package]]
 name = "wcwidth"
-version = "0.2.14"
+version = "0.2.13"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/24/30/6b0809f4510673dc723187aeaf24c7f5459922d01e2f794277a3dfb90345/wcwidth-0.2.14.tar.gz", hash = "sha256:4d478375d31bc5395a3c55c40ccdf3354688364cd61c4f6adacaa9215d0b3605", size = 102293, upload-time = "2025-09-22T16:29:53.023Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/6c/63/53559446a878410fc5a5974feb13d31d78d752eb18aeba59c7fef1af7598/wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5", size = 101301, upload-time = "2024-01-06T02:10:57.829Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/af/b5/123f13c975e9f27ab9c0770f514345bd406d0e8d3b7a0723af9d43f710af/wcwidth-0.2.14-py2.py3-none-any.whl", hash = "sha256:a7bb560c8aee30f9957e5f9895805edd20602f2d7f720186dfd906e82b4982e1", size = 37286, upload-time = "2025-09-22T16:29:51.641Z" },
+    { url = "https://files.pythonhosted.org/packages/fd/84/fd2ba7aafacbad3c4201d395674fc6348826569da3c0937e75505ead3528/wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859", size = 34166, upload-time = "2024-01-06T02:10:55.763Z" },
 ]
 
 [[package]]
@@ -4059,4 +4048,4 @@ source = { registry = "https://pypi.org/simple" }
 sdist = { url = "https://files.pythonhosted.org/packages/e3/02/0f2892c661036d50ede074e376733dca2ae7c6eb617489437771209d4180/zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166", size = 25547, upload-time = "2025-06-08T17:06:39.4Z" }
 wheels = [
     { url = "https://files.pythonhosted.org/packages/2e/54/647ade08bf0db230bfea292f893923872fd20be6ac6f53b2b936ba839d75/zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e", size = 10276, upload-time = "2025-06-08T17:06:38.034Z" },
-]
+]
\ No newline at end of file

From ac31e18a2498139347315a7ff8a7609882226270 Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Wed, 24 Sep 2025 19:42:24 +0000
Subject: [PATCH 22/24] Pre-commit

---
 uv.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/uv.lock b/uv.lock
index 1a745d44d..1de9b17fb 100644
--- a/uv.lock
+++ b/uv.lock
@@ -4048,4 +4048,4 @@ source = { registry = "https://pypi.org/simple" }
 sdist = { url = "https://files.pythonhosted.org/packages/e3/02/0f2892c661036d50ede074e376733dca2ae7c6eb617489437771209d4180/zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166", size = 25547, upload-time = "2025-06-08T17:06:39.4Z" }
 wheels = [
     { url = "https://files.pythonhosted.org/packages/2e/54/647ade08bf0db230bfea292f893923872fd20be6ac6f53b2b936ba839d75/zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e", size = 10276, upload-time = "2025-06-08T17:06:38.034Z" },
-]
\ No newline at end of file
+]

From e5305b8c98b6b2a7674f47d8c2ac424420bfc1db Mon Sep 17 00:00:00 2001
From: BrianMichell <brianm314@comcast.net>
Date: Tue, 30 Sep 2025 13:30:03 +0000
Subject: [PATCH 23/24] Remove raw field additions. Depends on segy >= 0.5.1

---
 src/mdio/converters/segy.py | 33 ------------------------------
 src/mdio/segy/creation.py   | 40 ++-----------------------------------
 2 files changed, 2 insertions(+), 71 deletions(-)

diff --git a/src/mdio/converters/segy.py b/src/mdio/converters/segy.py
index d5403b9c2..a96761c3c 100644
--- a/src/mdio/converters/segy.py
+++ b/src/mdio/converters/segy.py
@@ -4,15 +4,12 @@
 
 import logging
 import os
-from copy import deepcopy
 from typing import TYPE_CHECKING
 
 import numpy as np
 import zarr
 from segy import SegyFile
 from segy.config import SegySettings
-from segy.schema import HeaderField
-from segy.schema import ScalarType as ScalarType2
 from segy.standards.codes import MeasurementSystem as segy_MeasurementSystem
 from segy.standards.fields.trace import Rev0 as TraceHeaderFieldsRev0
 
@@ -344,33 +341,6 @@ def _add_grid_override_to_metadata(dataset: Dataset, grid_overrides: dict[str, A
         dataset.metadata.attributes["gridOverrides"] = grid_overrides
 
 
-def _scalar_to_size(scalar: ScalarType2) -> int:
-    # TODO(BrianMichell): #0000 Lazy way to support conversion.
-    if scalar == ScalarType2.STRING8:
-        return 8
-    try:
-        return int(str(scalar)[-2:]) // 8
-    except ValueError:
-        return 1
-
-
-def _customize_segy_spec(segy_spec: SegySpec) -> SegySpec:
-    assigned_bytes = []
-
-    ret = deepcopy(segy_spec)
-
-    for field in segy_spec.trace.header.fields:
-        byte = field.byte - 1
-        for i in range(byte, byte + _scalar_to_size(field.format)):
-            assigned_bytes.append(i)  # noqa: PERF402
-    unassigned_bytes = [i for i in range(240) if i not in assigned_bytes]
-    field_to_customize = [
-        HeaderField(name=f"__MDIO_RAW_UNSPECIFIED_Field_{i}", format=ScalarType.UINT8, byte=i + 1)
-        for i in unassigned_bytes
-    ]
-    return ret.customize(trace_header_fields=field_to_customize)
-
-
 def _add_raw_headers_to_template(mdio_template: AbstractDatasetTemplate) -> AbstractDatasetTemplate:
     """Add raw headers capability to the MDIO template by monkey-patching its _add_variables method.
 
@@ -451,9 +421,6 @@ def segy_to_mdio(  # noqa PLR0913
     input_path = _normalize_path(input_path)
     output_path = _normalize_path(output_path)
 
-    if os.getenv("MDIO__DO_RAW_HEADERS") == "1":
-        segy_spec = _customize_segy_spec(segy_spec)
-
     if not overwrite and output_path.exists():
         err = f"Output location '{output_path.as_posix()}' exists. Set `overwrite=True` if intended."
         raise FileExistsError(err)
diff --git a/src/mdio/segy/creation.py b/src/mdio/segy/creation.py
index 4c5e25a98..8b10ad486 100644
--- a/src/mdio/segy/creation.py
+++ b/src/mdio/segy/creation.py
@@ -28,38 +28,6 @@
 logger = logging.getLogger(__name__)
 
 
-def _filter_raw_unspecified_fields(headers: NDArray) -> NDArray:
-    """Filter out __MDIO_RAW_UNSPECIFIED_Field_* fields from headers array.
-
-    These fields are added during SEGY import to preserve raw header bytes,
-    but they cause dtype mismatches during export. This function removes them.
-
-    Args:
-        headers: Header array that may contain raw unspecified fields.
-
-    Returns:
-        Header array with raw unspecified fields removed.
-    """
-    if headers.dtype.names is None:
-        return headers
-
-    # Find field names that don't start with __MDIO_RAW_UNSPECIFIED_
-    field_names = [name for name in headers.dtype.names if not name.startswith("__MDIO_RAW_UNSPECIFIED_")]
-
-    if len(field_names) == len(headers.dtype.names):
-        # No raw unspecified fields found, return as-is
-        return headers
-
-    # Create new structured array with only the non-raw fields
-    new_dtype = [(name, headers.dtype.fields[name][0]) for name in field_names]
-    filtered_headers = np.empty(headers.shape, dtype=new_dtype)
-
-    for name in field_names:
-        filtered_headers[name] = headers[name]
-
-    return filtered_headers
-
-
 def make_segy_factory(spec: SegySpec, binary_header: dict[str, int]) -> SegyFactory:
     """Generate SEG-Y factory from MDIO metadata."""
     sample_interval = binary_header["sample_interval"]
@@ -199,9 +167,7 @@ def serialize_to_segy_stack(  # noqa: PLR0913
         samples = samples[live_mask]
         headers = headers[live_mask]
 
-        # Filter out raw unspecified fields that cause dtype mismatches
-        filtered_headers = _filter_raw_unspecified_fields(headers)
-        buffer = segy_factory.create_traces(filtered_headers, samples)
+        buffer = segy_factory.create_traces(headers, samples)
 
         global_index = block_start[0]
         record_id_str = str(global_index)
@@ -233,9 +199,7 @@ def serialize_to_segy_stack(  # noqa: PLR0913
             rec_samples = samples[rec_index][rec_live_mask]
             rec_headers = headers[rec_index][rec_live_mask]
 
-            # Filter out raw unspecified fields that cause dtype mismatches
-            filtered_headers = _filter_raw_unspecified_fields(rec_headers)
-            buffer = segy_factory.create_traces(filtered_headers, rec_samples)
+            buffer = segy_factory.create_traces(rec_headers, rec_samples)
 
             global_index = tuple(block_start[i] + rec_index[i] for i in range(record_ndim))
             record_id_str = "/".join(map(str, global_index))

From 817e0f985417cc6abef415c90f11c85bacf14e36 Mon Sep 17 00:00:00 2001
From: Brian Michell <brianm314@comcast.net>
Date: Tue, 30 Sep 2025 13:51:29 -0700
Subject: [PATCH 24/24] Removed raw byte inserts (#10)

* Update Xarray api access (#688)

* Reimplement disaster recovery logic

* Ensure getting true raw bytes for DR array

* Linting

* Add v2 issue check

* Fix pre-commit

* Profiled disaster recovery array (#8)

- Avoids duplicate read regression issue
- Implements isolated and testable logic

* Fix unclosed parenthesis

* Linting

* Test DR compatibility with all tested schemas

* Fix missing test fixture error

* Suppress unused linting error

* Attempt to use view

* Add hex-dump and MDIO output reproducer

* Fixes

* Cleanup

* Provide clean disaster recovery interface

* Begin work on tests

* Fix flattening issue

* Push for debugging

* Numpy updates

* Testing

* Working end-to-end examples

* Cleanup

* Bandaid fix

* linting pass 1

* Fix logic issue

* Use wrapper class

* Precommit

* Remove external debugging code

* Remove debug code

* Remove errant numpy additon to pyproject toml

* Fix uv lock to mainline

* Pre-commit

* Removed raw byte inserts

Removed the insertions of raw bytes into the raw bytes Variable. This issue will be addressed in tgsai/segy release >0.5.1

* Use new segy API calls

* Updates to get working

* Use released version

* Linting
---
 pyproject.toml                               |  4 +-
 src/mdio/api/io.py                           |  2 +-
 src/mdio/segy/_disaster_recovery_wrapper.py  | 22 +++++------
 src/mdio/segy/creation.py                    | 40 +++++++++++++++++++-
 tests/unit/test_disaster_recovery_wrapper.py | 36 ------------------
 uv.lock                                      | 22 +++++------
 6 files changed, 63 insertions(+), 63 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4a0dd004b..7d5a7e0bf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,10 +26,10 @@ dependencies = [
     "psutil>=7.0.0",
     "pydantic>=2.11.9",
     "rich>=14.1.0",
-    "segy>=0.5.0",
+    "segy>=0.5.1.post1",
     "tqdm>=4.67.1",
     "universal-pathlib>=0.2.6",
-    "xarray>=2025.9.0",
+    "xarray>=2025.9.1",
     "zarr>=3.1.3",
 ]
 
diff --git a/src/mdio/api/io.py b/src/mdio/api/io.py
index 862c66edd..2654be315 100644
--- a/src/mdio/api/io.py
+++ b/src/mdio/api/io.py
@@ -10,7 +10,7 @@
 from upath import UPath
 from xarray import Dataset as xr_Dataset
 from xarray import open_zarr as xr_open_zarr
-from xarray.backends.api import to_zarr as xr_to_zarr
+from xarray.backends.writers import to_zarr as xr_to_zarr
 
 from mdio.constants import ZarrFormat
 from mdio.core.zarr_io import zarr_warnings_suppress_unstable_structs_v3
diff --git a/src/mdio/segy/_disaster_recovery_wrapper.py b/src/mdio/segy/_disaster_recovery_wrapper.py
index aaa647731..282dfbedd 100644
--- a/src/mdio/segy/_disaster_recovery_wrapper.py
+++ b/src/mdio/segy/_disaster_recovery_wrapper.py
@@ -2,10 +2,8 @@
 
 from __future__ import annotations
 
-from copy import deepcopy
 from typing import TYPE_CHECKING
 
-import numpy as np
 
 if TYPE_CHECKING:
     from numpy.typing import NDArray
@@ -16,19 +14,21 @@ class SegyFileTraceDataWrapper:
     def __init__(self, segy_file: SegyFile, indices: int | list[int] | NDArray | slice):
         self.segy_file = segy_file
         self.indices = indices
-        self._header_pipeline = deepcopy(segy_file.accessors.header_decode_pipeline)
-        segy_file.accessors.header_decode_pipeline.transforms = []
-        self.traces = segy_file.trace[indices]
 
-    @property
-    def header(self) -> NDArray:
-        # The copy is necessary to avoid applying the pipeline to the original header.
-        return self._header_pipeline.apply(self.traces.header.copy())
+        self.idx = self.segy_file.trace.normalize_and_validate_query(self.indices)
+        self.traces = self.segy_file.trace.fetch(self.idx, raw=True)
+
+        self.raw_view = self.traces.view(self.segy_file.spec.trace.dtype)
+        self.decoded_traces = self.segy_file.accessors.trace_decode_pipeline.apply(self.raw_view.copy())
 
     @property
     def raw_header(self) -> NDArray:
-        return np.ascontiguousarray(self.traces.header.copy()).view("|V240")
+        return self.raw_view.header.view("|V240")
+
+    @property
+    def header(self) -> NDArray:
+        return self.decoded_traces.header
 
     @property
     def sample(self) -> NDArray:
-        return self.traces.sample
+        return self.decoded_traces.sample
diff --git a/src/mdio/segy/creation.py b/src/mdio/segy/creation.py
index 8b10ad486..4c5e25a98 100644
--- a/src/mdio/segy/creation.py
+++ b/src/mdio/segy/creation.py
@@ -28,6 +28,38 @@
 logger = logging.getLogger(__name__)
 
 
+def _filter_raw_unspecified_fields(headers: NDArray) -> NDArray:
+    """Filter out __MDIO_RAW_UNSPECIFIED_Field_* fields from headers array.
+
+    These fields are added during SEGY import to preserve raw header bytes,
+    but they cause dtype mismatches during export. This function removes them.
+
+    Args:
+        headers: Header array that may contain raw unspecified fields.
+
+    Returns:
+        Header array with raw unspecified fields removed.
+    """
+    if headers.dtype.names is None:
+        return headers
+
+    # Find field names that don't start with __MDIO_RAW_UNSPECIFIED_
+    field_names = [name for name in headers.dtype.names if not name.startswith("__MDIO_RAW_UNSPECIFIED_")]
+
+    if len(field_names) == len(headers.dtype.names):
+        # No raw unspecified fields found, return as-is
+        return headers
+
+    # Create new structured array with only the non-raw fields
+    new_dtype = [(name, headers.dtype.fields[name][0]) for name in field_names]
+    filtered_headers = np.empty(headers.shape, dtype=new_dtype)
+
+    for name in field_names:
+        filtered_headers[name] = headers[name]
+
+    return filtered_headers
+
+
 def make_segy_factory(spec: SegySpec, binary_header: dict[str, int]) -> SegyFactory:
     """Generate SEG-Y factory from MDIO metadata."""
     sample_interval = binary_header["sample_interval"]
@@ -167,7 +199,9 @@ def serialize_to_segy_stack(  # noqa: PLR0913
         samples = samples[live_mask]
         headers = headers[live_mask]
 
-        buffer = segy_factory.create_traces(headers, samples)
+        # Filter out raw unspecified fields that cause dtype mismatches
+        filtered_headers = _filter_raw_unspecified_fields(headers)
+        buffer = segy_factory.create_traces(filtered_headers, samples)
 
         global_index = block_start[0]
         record_id_str = str(global_index)
@@ -199,7 +233,9 @@ def serialize_to_segy_stack(  # noqa: PLR0913
             rec_samples = samples[rec_index][rec_live_mask]
             rec_headers = headers[rec_index][rec_live_mask]
 
-            buffer = segy_factory.create_traces(rec_headers, rec_samples)
+            # Filter out raw unspecified fields that cause dtype mismatches
+            filtered_headers = _filter_raw_unspecified_fields(rec_headers)
+            buffer = segy_factory.create_traces(filtered_headers, rec_samples)
 
             global_index = tuple(block_start[i] + rec_index[i] for i in range(record_ndim))
             record_id_str = "/".join(map(str, global_index))
diff --git a/tests/unit/test_disaster_recovery_wrapper.py b/tests/unit/test_disaster_recovery_wrapper.py
index bb1864f67..4edee6752 100644
--- a/tests/unit/test_disaster_recovery_wrapper.py
+++ b/tests/unit/test_disaster_recovery_wrapper.py
@@ -287,39 +287,3 @@ def test_different_index_types(
             expected_count = 1
 
         assert wrapper.header.size == expected_count
-
-    def test_header_pipeline_preservation(self, temp_dir: Path, basic_segy_spec: SegySpec, segy_config: dict) -> None:
-        """Test that the wrapper preserves the original header pipeline."""
-        config_name = segy_config["name"]
-        endianness = segy_config["endianness"]
-        data_format = segy_config["data_format"]
-
-        segy_path = temp_dir / f"test_pipeline_{config_name}.segy"
-
-        # Create test SEGY file
-        num_traces = 5
-        samples_per_trace = SAMPLES_PER_TRACE
-
-        spec = self.create_test_segy_file(
-            spec=basic_segy_spec,
-            num_traces=num_traces,
-            samples_per_trace=samples_per_trace,
-            output_path=segy_path,
-            endianness=endianness,
-            data_format=data_format,
-        )
-
-        # Load the SEGY file
-        segy_file = SegyFile(segy_path, spec=spec)
-
-        # Store original pipeline transforms count
-        original_transforms_count = len(segy_file.accessors.header_decode_pipeline.transforms)
-
-        # Create wrapper
-        wrapper = SegyFileTraceDataWrapper(segy_file, 0)
-
-        # Verify that the original SEGY file's pipeline was modified (transforms cleared)
-        assert len(segy_file.accessors.header_decode_pipeline.transforms) == 0
-
-        # Verify that the wrapper has its own pipeline with the original transforms
-        assert len(wrapper._header_pipeline.transforms) == original_transforms_count
diff --git a/uv.lock b/uv.lock
index 1de9b17fb..f73fa0d2a 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1922,10 +1922,10 @@ requires-dist = [
     { name = "pydantic", specifier = ">=2.11.9" },
     { name = "rich", specifier = ">=14.1.0" },
     { name = "s3fs", marker = "extra == 'cloud'", specifier = ">=2025.9.0" },
-    { name = "segy", specifier = ">=0.5.0" },
+    { name = "segy", specifier = ">=0.5.1.post1" },
     { name = "tqdm", specifier = ">=4.67.1" },
     { name = "universal-pathlib", specifier = ">=0.2.6" },
-    { name = "xarray", specifier = ">=2025.9.0" },
+    { name = "xarray", specifier = ">=2025.9.1" },
     { name = "zarr", specifier = ">=3.1.3" },
     { name = "zfpy", marker = "extra == 'lossy'", specifier = ">=1.0.1" },
 ]
@@ -3198,7 +3198,7 @@ wheels = [
 
 [[package]]
 name = "segy"
-version = "0.5.0.post1"
+version = "0.5.1.post1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "fsspec" },
@@ -3210,9 +3210,9 @@ dependencies = [
     { name = "rapidfuzz" },
     { name = "typer" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/65/c2/aae81f9f9ae43c28c2d6b543719e6f1805d50d9565f3616af9ce29e3fbc0/segy-0.5.0.post1.tar.gz", hash = "sha256:b8c140fb10cfd4807bc6aab46a6f09d98b82c4995e045f568be3bbf6c044aba6", size = 43037, upload-time = "2025-09-15T13:33:42.348Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/0a/c5/c71d4f52eb1587bdeb8401445ac65b08603fb6f77ada46933dec5fbbd6f8/segy-0.5.1.post1.tar.gz", hash = "sha256:655d1b26aa7a698084d190c8b5c7d12802cfbc9627067614606b1d69c5f0f4ae", size = 43354, upload-time = "2025-09-30T20:35:19.879Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/27/f0/b67a8a89dbb331d55e9b37c779c270a48ff09ca83a0055a65a84f33dc100/segy-0.5.0.post1-py3-none-any.whl", hash = "sha256:158661da578147fa5cfbcf335047a2459f86aa5522e1acc4249bb8252d26be55", size = 55408, upload-time = "2025-09-15T13:33:40.571Z" },
+    { url = "https://files.pythonhosted.org/packages/71/ff/ee1b5c982ddfb7185fac41b85ce7a8bd2d5604d6129183a63c2a851109d3/segy-0.5.1.post1-py3-none-any.whl", hash = "sha256:6f36a0795c459d77a3d715d7e5b1444be4cb8368720f89111d452be93d1cf7f1", size = 55757, upload-time = "2025-09-30T20:35:18.665Z" },
 ]
 
 [[package]]
@@ -3611,7 +3611,7 @@ wheels = [
 
 [[package]]
 name = "typer"
-version = "0.16.1"
+version = "0.19.2"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "click" },
@@ -3619,9 +3619,9 @@ dependencies = [
     { name = "shellingham" },
     { name = "typing-extensions" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/43/78/d90f616bf5f88f8710ad067c1f8705bf7618059836ca084e5bb2a0855d75/typer-0.16.1.tar.gz", hash = "sha256:d358c65a464a7a90f338e3bb7ff0c74ac081449e53884b12ba658cbd72990614", size = 102836, upload-time = "2025-08-18T19:18:22.898Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/21/ca/950278884e2ca20547ff3eb109478c6baf6b8cf219318e6bc4f666fad8e8/typer-0.19.2.tar.gz", hash = "sha256:9ad824308ded0ad06cc716434705f691d4ee0bfd0fb081839d2e426860e7fdca", size = 104755, upload-time = "2025-09-23T09:47:48.256Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/2d/76/06dbe78f39b2203d2a47d5facc5df5102d0561e2807396471b5f7c5a30a1/typer-0.16.1-py3-none-any.whl", hash = "sha256:90ee01cb02d9b8395ae21ee3368421faf21fa138cb2a541ed369c08cec5237c9", size = 46397, upload-time = "2025-08-18T19:18:21.663Z" },
+    { url = "https://files.pythonhosted.org/packages/00/22/35617eee79080a5d071d0f14ad698d325ee6b3bf824fc0467c03b30e7fa8/typer-0.19.2-py3-none-any.whl", hash = "sha256:755e7e19670ffad8283db353267cb81ef252f595aa6834a0d1ca9312d9326cb9", size = 46748, upload-time = "2025-09-23T09:47:46.777Z" },
 ]
 
 [[package]]
@@ -3876,16 +3876,16 @@ wheels = [
 
 [[package]]
 name = "xarray"
-version = "2025.9.0"
+version = "2025.9.1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "numpy" },
     { name = "packaging" },
     { name = "pandas" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/4e/0b/bbb76e05c8e2099baf90e259c29cafe6a525524b1d1da8bfbc39577c043e/xarray-2025.9.0.tar.gz", hash = "sha256:7dd6816fe0062c49c5e9370dd483843bc13e5ed80a47a9ff10baff2b51e070fb", size = 3040318, upload-time = "2025-09-04T04:20:26.296Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/d0/5d/e139112a463336c636d4455494f3227b7f47a2e06ca7571e6b88158ffc06/xarray-2025.9.1.tar.gz", hash = "sha256:f34a27a52c13d1f3cceb7b27276aeec47021558363617dd7ef4f4c8b379011c0", size = 3057322, upload-time = "2025-09-30T05:28:53.084Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/8d/f0/73c24457c941b8b08f7d090853e40f4b2cdde88b5da721f3f28e98df77c9/xarray-2025.9.0-py3-none-any.whl", hash = "sha256:79f0e25fb39571f612526ee998ee5404d8725a1db3951aabffdb287388885df0", size = 1349595, upload-time = "2025-09-04T04:20:24.36Z" },
+    { url = "https://files.pythonhosted.org/packages/0e/a7/6eeb32e705d510a672f74135f538ad27f87f3d600845bfd3834ea3a77c7e/xarray-2025.9.1-py3-none-any.whl", hash = "sha256:3e9708db0d7915c784ed6c227d81b398dca4957afe68d119481f8a448fc88c44", size = 1364411, upload-time = "2025-09-30T05:28:51.294Z" },
 ]
 
 [[package]]