Restructured Input Arguments for Examples

EX01_loadMeasurement.py

@@ -1,34 +1,16 @@
 import os
 import platform
+from pathlib import Path
 
 import matplotlib.pyplot as plt
 import numpy as np
 
 import cuvis
 
-### default directories and files
-data_dir = None
-
-if platform.system() == "Windows":
-    lib_dir = os.getenv("CUVIS")
-    data_dir = os.path.normpath(os.path.join(lib_dir, os.path.pardir, "sdk",
-                                             "sample_data", "set_examples"))
-elif platform.system() == "Linux":
-    lib_dir = os.getenv("CUVIS_DATA")
-    data_dir = os.path.normpath(
-        os.path.join(lib_dir, "sample_data", "set_examples"))
-
-# default image
-loc_file = os.path.join(data_dir,
-                        "set0_single",
-                        "single.cu3s")
-# default settings
-loc_settings = os.path.join(data_dir, "settings")
-
 
 def run_example_loadMeasurement(
-        userSettingsDir=loc_settings,
-        measurementLoc=loc_file):
+        userSettingsDir,
+        measurementLoc):
     print("loading user settings...")
     cuvis.init(userSettingsDir)
     cuvis.set_log_level("info")
@@ -44,13 +26,13 @@ def run_example_loadMeasurement(
                                             mesu.integration_time,
                                             mesu.processing_mode.name,
                                             ))
-    
+
     if isinstance(mesu.measurement_flags, cuvis.MeasurementFlags):
         print(f"Flags: {mesu.measurement_flags}")
         for v in cuvis.MeasurementFlags.supremum():
             print(f'{v}: {v in mesu.measurement_flags}')
 
-    cube = mesu.data.get("cube", None)
+    cube = mesu.cube
     if cube is None:
         raise Exception("Cube not found")
 
@@ -78,6 +60,20 @@ def run_example_loadMeasurement(
 
 if __name__ == "__main__":
 
+    if platform.system() == "Windows":
+        data_dir = Path(os.getenv("CUVIS")).parent / "sdk" / \
+            "sample_data" / "set_examples"
+
+    elif platform.system() == "Linux":
+        data_dir = Path(os.getenv("CUVIS_DATA")) / \
+            "sample_data" / "set_examples"
+
+    # default image
+    loc_file = data_dir / "set0_single" / "single.cu3s"
+
+    # default settings
+    loc_settings = data_dir / "settings"
+
     print("Example 01: Load Measurement. Please provide:")
 
     userSettingsDir = input(
@@ -90,4 +86,4 @@ def run_example_loadMeasurement(
     if measurementLoc.strip().lower() in ["", "default"]:
         measurementLoc = loc_file
 
-    run_example_loadMeasurement(userSettingsDir, measurementLoc)
+    run_example_loadMeasurement(str(userSettingsDir), str(measurementLoc))

EX02_reprocessMeasurement.py

@@ -1,48 +1,17 @@
 import os
 import platform
+from pathlib import Path
 
 import cuvis
 
-### default directories and files
-data_dir = None
-
-if platform.system() == "Windows":
-    lib_dir = os.getenv("CUVIS")
-    data_dir = os.path.normpath(os.path.join(lib_dir, os.path.pardir, "sdk",
-                                             "sample_data", "set_examples"))
-elif platform.system() == "Linux":
-    lib_dir = os.getenv("CUVIS_DATA")
-    data_dir = os.path.normpath(
-        os.path.join(lib_dir, "sample_data", "set_examples"))
-
-# default images
-loc_file = os.path.join(data_dir,
-                        "set0_single",
-                        "single_raw.cu3s")
-loc_dark = os.path.join(data_dir,
-                        "set0_single",
-                        "single_dark.cu3s")
-loc_white = os.path.join(data_dir,
-                         "set0_single",
-                         "single_white.cu3s")
-loc_distance = os.path.join(data_dir,
-                            "set0_single",
-                            "single_distance.cu3s")
-
-# default settings
-loc_settings = os.path.join(data_dir, "settings")
-
-# default output
-loc_output = os.path.join(os.getcwd(), "EX02_reprocessed")
-
 
 def run_example_reprocessMeasurement(
-        userSettingsDir=loc_settings,
-        measurementLoc=loc_file,
-        darkLoc=loc_dark,
-        whiteLoc=loc_white,
-        distanceLoc=loc_distance,
-        outDir=loc_output):
+        userSettingsDir,
+        measurementLoc,
+        darkLoc,
+        whiteLoc,
+        distanceLoc,
+        outDir):
     print("loading user settings...")
     cuvis.init(userSettingsDir)
     cuvis.set_log_level("info")
@@ -82,8 +51,8 @@ def run_example_reprocessMeasurement(
 
     procArgs = cuvis.ProcessingArgs()
     saveArgs = cuvis.SaveArgs(allow_overwrite=True,
-                                    allow_session_file=True,
-                                    allow_info_file=False)
+                              allow_session_file=True,
+                              allow_info_file=False)
 
     modes = [cuvis.ProcessingMode.Raw,
              cuvis.ProcessingMode.DarkSubtract,
@@ -99,8 +68,8 @@ def run_example_reprocessMeasurement(
             print("processing to mode {}...".format(mode))
             processingContext.set_processing_args(procArgs)
             mesu = processingContext.apply(mesu)
-            mesu.set_name(mode)
-            saveArgs.export_dir = os.path.join(outDir, mode)
+            mesu.set_name(mode.name)
+            saveArgs.export_dir = str(Path(outDir) / mode.name)
             exporter = cuvis.Export.CubeExporter(saveArgs)
             exporter.apply(mesu)
 
@@ -113,7 +82,29 @@ def run_example_reprocessMeasurement(
 
 if __name__ == "__main__":
 
-    print("Example 02: Reprocess Measurement. Please provide:")
+    if platform.system() == "Windows":
+        data_dir = Path(os.getenv("CUVIS")).parent / "sdk" / \
+            "sample_data" / "set_examples"
+
+    elif platform.system() == "Linux":
+        data_dir = Path(os.getenv("CUVIS_DATA")) / \
+            "sample_data" / "set_examples"
+
+    # default images
+    loc_file = data_dir / "set0_single" / "single_raw.cu3s"
+    loc_dark = data_dir / "set0_single" / "single_dark.cu3s"
+    loc_white = data_dir / "set0_single" / "single_white.cu3s"
+
+    loc_distance = data_dir / "set0_single" / "single_distance.cu3s"
+
+    # default settings
+    loc_settings = data_dir / "settings"
+
+    # default output
+    loc_output = Path(os.getcwd()) / "EX02_reprocessed"
+
+    print(
+        "Example 02: Reprocess Measurement. Please provide:")
 
     userSettingsDir = input(
         "User settings directory (default: {}): ".format(loc_settings))
@@ -143,9 +134,9 @@ def run_example_reprocessMeasurement(
     if outDir.strip().lower() in ["", "default"]:
         outDir = loc_output
 
-    run_example_reprocessMeasurement(userSettingsDir,
-                                     measurementLoc,
-                                     darkLoc,
-                                     whiteLoc,
-                                     distanceLoc,
-                                     outDir)
+    run_example_reprocessMeasurement(str(userSettingsDir),
+                                     str(measurementLoc),
+                                     str(darkLoc),
+                                     str(whiteLoc),
+                                     str(distanceLoc),
+                                     str(outDir))

EX03_exportMeasurement.py

@@ -1,45 +1,14 @@
 import os
 import platform
+from pathlib import Path
 
 import cuvis
 
-### default directories and files
-data_dir = None
-plugin_dir = None
-
-if platform.system() == "Windows":
-    lib_dir = os.getenv("CUVIS")
-    data_dir = os.path.normpath(os.path.join(lib_dir, os.path.pardir, "sdk",
-                                             "sample_data", "set_examples"))
-    plugin_dir = os.path.normpath(os.path.join(lib_dir, os.path.pardir, "sdk",
-                                               "sample_data", "set_examples",
-                                               "userplugin"))
-
-elif platform.system() == "Linux":
-    lib_dir = os.getenv("CUVIS_DATA")
-    data_dir = os.path.normpath(
-        os.path.join(lib_dir, "sample_data", "set_examples"))
-    plugin_dir = os.path.normpath(os.path.join(lib_dir, "sdk",
-                                               "sample_data", "set_examples",
-                                               "plugin"))
-
-# default images
-loc_file = os.path.join(data_dir,
-                        "set0_single",
-                        "single.cu3s")
-loc_plugin = os.path.join(plugin_dir,"ref", "cai.xml")
-
-# default settings
-loc_settings = os.path.join(data_dir, "settings")
-
-# default output
-loc_output = os.path.join(os.getcwd(), "EX03_export")
-
-
-def run_example_exportMeasurement(userSettingsDir=loc_settings,
-                                  measurementLoc=loc_file,
-                                  pluginLoc=loc_plugin,
-                                  exportDir=loc_output):
+
+def run_example_exportMeasurement(userSettingsDir,
+                                  measurementLoc,
+                                  pluginLoc,
+                                  exportDir):
     print("loading user settings...")
     cuvis.init(userSettingsDir)
     cuvis.set_log_level("info")
@@ -60,13 +29,13 @@ def run_example_exportMeasurement(userSettingsDir=loc_settings,
 
     print("Export to Multi-Channel Tiff...")
     multi_tiff_settings = cuvis.TiffExportSettings(
-        export_dir=os.path.join(exportDir, "multi"), format="MultiChannel")
+        export_dir=os.path.join(exportDir, "multi"), format=cuvis.TiffFormat.MultiChannel)
     multiTiffExporter = cuvis.TiffExporter(multi_tiff_settings)
     multiTiffExporter.apply(mesu)
 
     print("Export to separate Tiffs...")
     single_tiff_settings = cuvis.TiffExportSettings(
-        export_dir=os.path.join(exportDir, "single"), format="Single")
+        export_dir=os.path.join(exportDir, "single"), format=cuvis.TiffFormat.Single)
     singleTiffExporter = cuvis.TiffExporter(single_tiff_settings)
     singleTiffExporter.apply(mesu)
 
@@ -90,6 +59,28 @@ def run_example_exportMeasurement(userSettingsDir=loc_settings,
 
 if __name__ == "__main__":
 
+    if platform.system() == "Windows":
+        lib_dir = Path(os.getenv("CUVIS"))
+        data_dir = lib_dir.parent / "sdk" / \
+            "sample_data" / "set_examples"
+        plugin_dir = lib_dir.parent / "user" / "plugin"
+
+    elif platform.system() == "Linux":
+        lib_dir = Path(os.getenv("CUVIS_DATA"))
+        data_dir = lib_dir / \
+            "sample_data" / "set_examples"
+        plugin_dir = lib_dir / "user" / "plugin"
+
+    # default images
+    loc_file = data_dir / "set0_single" / "single.cu3s"
+    loc_plugin = plugin_dir / "ref" / "cai.xml"
+
+    # default settings
+    loc_settings = data_dir / "settings"
+
+    # default output
+    loc_output = Path(os.getcwd()) / "EX03_export"
+
     print("Example 03: Export Measurement. Please provide:")
 
     userSettingsDir = input(
@@ -112,5 +103,5 @@ def run_example_exportMeasurement(userSettingsDir=loc_settings,
     if exportDir.strip().lower() in ["", "default"]:
         exportDir = loc_output
 
-    run_example_exportMeasurement(userSettingsDir, measurementLoc, pluginLoc,
-                                  exportDir)
+    run_example_exportMeasurement(str(userSettingsDir), str(measurementLoc), str(pluginLoc),
+                                  str(exportDir))