Merge pull request #82 from Sparks29032/morph_sequence

Add functionality for multiple morphs in one command

Author: sbillinge

.github/workflows/main.yml

@@ -53,4 +53,3 @@ jobs:
           coverage run run_tests.py
           coverage report -m
           codecov
-

diffpy/pdfmorph/__init__.py

@@ -17,9 +17,12 @@
 """
 
 # obtain version information
-__version__ = '0.0.1'
+from diffpy.pdfmorph.version import __version__
 
 # top-level import
 from diffpy.pdfmorph.pdfmorph_api import pdfmorph, morph_default_config, plot_morph
 
+# key used when saving multiple morphs
+__save_morph_as__ = "save_morph_as"
+
 # End of file

diffpy/pdfmorph/morph_helpers/transformrdftopdf.py

@@ -18,6 +18,7 @@
 """
 
 
+import numpy
 from diffpy.pdfmorph.morphs.morph import *
 
 
@@ -50,12 +51,12 @@ def morph(self, x_morph, y_morph, x_target, y_target):
         Morph.morph(self, x_morph, y_morph, x_target, y_target)
         morph_baseline = self.baselineslope * self.x_morph_in
         target_baseline = self.baselineslope * self.x_target_in
-        self.y_target_out = self.y_target_in / self.x_target_in + target_baseline
-        if self.x_target_in[0] == 0:
-            self.y_target_out[0] = 0
-        self.y_morph_out = self.y_morph_in / self.x_morph_in + morph_baseline
-        if self.x_morph_in[0] == 0:
-            self.y_morph_out[0] = 0
+        with numpy.errstate(divide='ignore', invalid='ignore'):
+            self.y_target_out = self.y_target_in / self.x_target_in + target_baseline
+        self.y_target_out[self.x_target_in == 0] = 0
+        with numpy.errstate(divide='ignore', invalid='ignore'):
+            self.y_morph_out = self.y_morph_in / self.x_morph_in + morph_baseline
+        self.y_morph_out[self.x_target_in == 0] = 0
         return self.xyallout
 
 

diffpy/pdfmorph/pdfmorph_io.py

@@ -0,0 +1,235 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.pdfmorph   by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2010 Trustees of the Columbia University
+#                   in the City of New York.  All rights reserved.
+#
+# File coded by:
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE.txt for license information.
+#
+##############################################################################
+
+
+from __future__ import print_function
+
+import sys
+from pathlib import Path
+
+import numpy
+
+from diffpy.pdfmorph import __save_morph_as__
+import diffpy.pdfmorph.tools as tools
+
+
+def single_morph_output(morph_inputs, morph_results,
+                        save_file=None, morph_file=None, xy_out=None,
+                        verbose=False, stdout_flag=False):
+    """Helper function for printing details about a single morph.
+    Handles both printing to terminal and printing to a file.
+
+    :param morph_inputs:    Dictionary of parameters given by the user.
+    :param morph_results:   Dictionary of resulting data after morphing.
+    :param save_file:       name of file to print to. If None (defualt) print to terminal.
+    :param morph_file:      name of the morphed PDF file. Required when printing to a non-terminal file.
+    :param xy_out:          List of the form [x_morph_out, y_morph_out]. x_morph_out is a List of r values
+                            and y_morph_out is a List of gr values.
+    :param verbose:         print additional details about the morph when True (default False).
+    :param stdout_flag:     print to terminal when True (default False).
+    """
+
+    # Input and output parameters
+    morphs_in = "\n# Input morphing parameters:\n"
+    morphs_in += "\n".join(f"# {key} = {morph_inputs[key]}" for key in morph_inputs.keys()) + "\n"
+
+    morphs_out = "# Optimized morphing parameters:\n"
+    morphs_out += "\n".join(f"# {key} = {morph_results[key]:.6f}" for key in morph_results.keys())
+
+    # Printing to terminal
+    if stdout_flag:
+        print(f"{morphs_in}\n{morphs_out}\n")
+
+    # Saving to file
+    if save_file is not None:
+        path_name = str(Path(morph_file).resolve())
+        header = "# PDF created by pdfmorph\n"
+        header += f"# from {path_name}"
+
+        header_verbose = f"{morphs_in}\n{morphs_out}"
+
+        if save_file != "-":
+            with open(save_file, 'w') as outfile:
+                # Print out a header (more if verbose)
+                print(header, file=outfile)
+                if verbose:
+                    print(header_verbose, file=outfile)
+
+                # Print table with label
+                print("\n# Labels: [r] [gr]", file=outfile)
+                numpy.savetxt(outfile, numpy.transpose(xy_out))
+
+            if stdout_flag:
+                # Indicate successful save
+                save_message = f"# Morph saved to {save_file}\n"
+                print(save_message)
+
+        else:
+            # Just print table with label if save is to stdout
+            print("# Labels: [r] [gr]")
+            numpy.savetxt(sys.stdout, numpy.transpose(xy_out))
+
+
+def create_morphs_directory(save_directory):
+    """Create a directory for saving multiple morphed PDFs.
+
+    Takes in a user-given path to a directory save_directory and create a subdirectory named Morphs.
+    PDFmorph will save all morphs into the Morphs subdirectory while metadata about the morphs will
+    be stored in save_directory outside Morphs.
+
+    :param save_directory:  path to a directory. PDFmorph will save all generated files within
+                            this directory.
+
+    :return: Returns the absolute path to the Morph subdirectory as a string.
+    """
+    # Make directory to save files in if it does not already exist
+    Path(save_directory).mkdir(parents=True, exist_ok=True)
+
+    # Morphs will be saved in the subdirectory "Morphs"
+    morphs_subdirectory = Path(save_directory).joinpath("Morphs")
+    morphs_subdirectory.mkdir(exist_ok=True)
+
+    return str(morphs_subdirectory.resolve())
+
+
+def get_multisave_names(target_list: list, save_names_file=None):
+    """Create or import a dictionary that specifies names to save morphs as.
+    First attempt to import names from a specified file. If names for certain morphs not found,
+    use default naming scheme: 'Morph_with_Target_<target file name>.cgr'.
+
+    Used when saving multiple morphs.
+
+    :param target_list:     List of target PDFs used for each morph.
+    :param save_names_file: name of file to import save names dictionary from (default None).
+
+    :return: Returns a dictionary containing names to save each morph as. Keys are the target
+             PDF file names used to produce that morph.
+    """
+
+    # Dictionary storing save file names
+    save_names = {}
+
+    # Import names from a serial file
+    if save_names_file is not None:
+        # Names should be stored properly in save_names_file
+        save_names = tools.deserialize(save_names_file)
+    # Apply default naming scheme to missing targets
+    for target_file in target_list:
+        if target_file.name not in save_names.keys():
+            save_names.update({target_file.name:
+                                   {__save_morph_as__: f"Morph_with_Target_{target_file.stem}.cgr"}})
+    return save_names
+
+
+def multiple_morph_output(morph_inputs, morph_results, target_files,
+                          field=None, field_list=None,
+                          save_directory=None, morph_file=None, target_directory=None,
+                          verbose=False, stdout_flag=False):
+    """Helper function for printing details about a series of multiple morphs.
+    Handles both printing to terminal and printing to a file.
+
+    :param morph_inputs:        Dictionary of parameters given by the user.
+    :param morph_results:       Dictionary of resulting data after morphing.
+    :param target_files:        List of PDF files that acted as targets to morphs.
+    :param save_directory:      name of directory to save morphs in.
+    :param field:               name of field if data was sorted by a particular field. Otherwise, leave
+                                blank.
+    :param field_list:          List of field values for each target PDF. Generated by
+                                diffpy.pdfmorph.tools.field_sort().
+    :param morph_file:          name of the morphed PDF file. Required to give summary data after saving
+                                to a directory.
+    :param target_directory:    name of the directory containing the target PDF files. Required to give
+                                summary data after saving to a directory.
+    :param verbose:             print additional summary details when True (default False).
+    :param stdout_flag:         print to terminal when True (default False).
+    """
+
+    # Input parameters used for every morph
+    inputs = "\n# Input morphing parameters:\n"
+    inputs += "\n".join(f"# {key} = {morph_inputs[key]}" for key in morph_inputs.keys())
+
+    # Verbose to get output for every morph
+    verbose_outputs = ""
+    if verbose:
+        # Output for every morph (information repeated in a succinct table below)
+        for target in morph_results.keys():
+            output = f"\n# Target: {target}\n"
+            output += "# Optimized morphing parameters:\n"
+            output += "\n".join(f"# {param} = {morph_results[target][param]:.6f}" for param in morph_results[target])
+            verbose_outputs += f"{output}\n"
+
+    # Get items we want to put in table
+    tabulated_results = tabulate_results(morph_results)
+
+    # Table labels
+    labels = "\n# Labels: [Target]"
+    if field is not None:
+        labels += f" [{field}]"
+    for param in tabulated_results.keys():
+        if len(tabulated_results[param]) > 0:
+            labels += f" [{param}]"
+
+    # Corresponding table
+    table = f"{labels}\n"
+    for idx in range(len(target_files)):
+        row = f"{target_files[idx]}"
+        if field_list is not None:
+            row += f" {field_list[idx]}"
+        for param in tabulated_results.keys():
+            if len(tabulated_results[param]) > idx:
+                row += f" {tabulated_results[param][idx]:0.6f}"
+        table += f"{row}\n"
+    table = table[:-1]  # Remove extra indent
+
+    # Printing summary to terminal
+    if stdout_flag:
+        print(f"{inputs}\n{verbose_outputs}{table}\n")
+
+    # Saving summary as a file
+    if save_directory is not None:
+        morph_path_name = str(Path(morph_file).resolve())
+        target_path_name = str(Path(target_directory).resolve())
+
+        header = "# Data generated by pdfmorph\n"
+        header += f"# from morphing {morph_path_name}\n"
+        header += f"# with target directory {target_path_name}"
+        reference_table = Path(save_directory).joinpath("Morph_Reference_Table.csv")
+        with open(reference_table, 'w') as reference:
+            print(f"{header}\n{inputs}\n{verbose_outputs}{table}", file=reference)
+
+        if stdout_flag:
+            # Indicate successful save
+            save_message = f"# Morphs saved in the directory {save_directory}\n"
+            print(save_message)
+
+
+def tabulate_results(multiple_morph_results):
+    """Helper function to make a data table summarizing details about the results of multiple morphs.
+
+    :param multiple_morph_results:  collection of Dictionaries. Each Dictionary summarizes the results
+                                    of a single morph.
+
+    :return: Returns a Dictionary tabulated_results. Keys in tabulated_results are the table's column names
+    and each corresponding value is a List of data for that column.
+    """
+
+    # We only care about the following parameters in our data tables
+    relevant_parameters = ["Scale", "Smear", "Stretch", "Pearson", "Rw"]
+
+    # Keys in this table represent column names and the value will be a list of column data
+    tabulated_results = {}
+    for param in relevant_parameters:
+        tabulated_results.update({param: tools.get_values_from_dictionary_collection(multiple_morph_results, param)})
+    return tabulated_results