Allow choice of plot parameter, some reformatting

Sparks29032 · Sparks29032 · commit f7fe9811e524 · 2023-10-13T17:22:31.000-04:00
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -46,18 +46,6 @@ jobs:
           conda install --file requirements/test.txt
           pip install .
 
-      # redownload diffpy.utils pre 3.2.0 release, use https since public repo
-      - name: install diffpy.utils
-        shell: bash -l {0}
-        run: |
-          git clone https://github.com/diffpy/diffpy.utils.git
-          cd diffpy.utils
-          rm run_tests.py
-          rm -r conda-recipe
-          rm -r src/diffpy/utils/tests
-          conda activate test
-          pip install .
-
       - name: Validate pdfmorph
         shell: bash -l {0}
         run: |
diff --git a/diffpy/pdfmorph/pdfmorph_api.py b/diffpy/pdfmorph/pdfmorph_api.py
@@ -212,7 +212,7 @@ def pdfmorph(
             if "scale" in refpars:
                 rptemp.append("scale")
             refiner.refine(*rptemp)
-        # Refine all params
+        # Refine all param_list
         refiner.refine(*refpars)
     else:
         # no operation if refine=False or refpars is empty list
diff --git a/diffpy/pdfmorph/pdfmorphapp.py b/diffpy/pdfmorph/pdfmorphapp.py
@@ -67,18 +67,6 @@ def custom_error(self, msg):
         help="""Save the manipulated PDF to a file named NAME. Use \'-\' for stdout.
 When --multiple is enabled, save each manipulated PDF as a file in a directory named NAME;
 you can specify names for each saved PDF file using --save-names-file.""",
-    )
-    parser.add_option(
-        '--snf',
-        '--save-names-file',
-        metavar="NAMESFILE",
-        dest="snamesfile",
-        help=f"""Used only when both -s and --multiple are enabled.
-Specify names for each manipulated PDF when saving (see -s) using a serial file
-NAMESFILE. The format of NAMESFILE should be as follows: each target PDF
-is an entry in NAMESFILE. For each entry, there should be a key {__save_morph_as__}
-whose value specifies the name to save the manipulated PDF as.
-(See sample names files in the PDFmorph tutorial).""",
     )
     parser.add_option(
         '-v',
@@ -88,53 +76,82 @@ def custom_error(self, msg):
         help="Print additional header details to saved files.",
     )
     parser.add_option(
+        '--rmin', type="float", help="Minimum r-value to use for PDF comparisons."
+    )
+    parser.add_option(
+        '--rmax', type="float", help="Maximum r-value to use for PDF comparisons."
+    )
+    parser.add_option(
+        '--pearson',
+        action="store_true",
+        dest="pearson",
+        help="Maximize agreement in the Pearson function. Note that this is insensitive to scale.",
+    )
+    parser.add_option(
+        '--addpearson',
+        action="store_true",
+        dest="addpearson",
+        help="""Maximize agreement in the Pearson function as well as
+minimizing the residual.""",
+    )
+
+    group = optparse.OptionGroup(
+        parser,
+        "Multiple Morphs",
+        """This program can morph a PDF against multiple targets in one command.
+See -s and Plot Options for how saving and plotting functionality changes when performing multiple morphs."""
+    )
+    parser.add_option_group(group)
+    group.add_option(
         '--multiple',
         dest="multiple",
         action="store_true",
         help=f"""Changes usage to \'{prog_short} [options] FILE DIRECTORY\'. FILE
 will be morphed with each file in DIRECTORY as target.
 Files in DIRECTORY are sorted by alphabetical order unless a field is
-specified by --sort-by. See -s and Plot Options for how saving and
-plotting change when this option is enabled.""",
+specified by --sort-by.""",
     )
-    parser.add_option(
+    group.add_option(
         '--sort-by',
         metavar="FIELD",
         dest="field",
         help="""Used with --multiple to sort files in DIRECTORY by FIELD from lowest to highest.
 FIELD must be included in the header of all the PDF files.""",
     )
-    parser.add_option(
+    group.add_option(
         '--reverse',
         dest="reverse",
         action="store_true",
         help="""Sort from highest to lowest instead.""",
     )
-    parser.add_option(
+    group.add_option(
         '--serial-file',
-        metavar="SERIAL",
+        metavar="SERIALFILE",
         dest="serfile",
         help="""Look for FIELD in a serial file instead.
-Must specify name of serial file SERIAL.""",
-    )
-    parser.add_option(
-        '--rmin', type="float", help="Minimum r-value to use for PDF comparisons."
+Must specify name of serial file SERIALFILE.""",
     )
-    parser.add_option(
-        '--rmax', type="float", help="Maximum r-value to use for PDF comparisons."
-    )
-    parser.add_option(
-        '--pearson',
-        action="store_true",
-        dest="pearson",
-        help="Maximize agreement in the Pearson function. Note that this is insensitive to scale.",
+    group.add_option(
+        '--save-names-file',
+        metavar="NAMESFILE",
+        dest="snamesfile",
+        help=f"""Used when both -s and --multiple are enabled.
+Specify names for each manipulated PDF when saving (see -s) using a serial file
+NAMESFILE. The format of NAMESFILE should be as follows: each target PDF
+is an entry in NAMESFILE. For each entry, there should be a key {__save_morph_as__}
+whose value specifies the name to save the manipulated PDF as.
+(See sample names files in the PDFmorph tutorial).""",
     )
-    parser.add_option(
-        '--addpearson',
-        action="store_true",
-        dest="addpearson",
-        help="""Maximize agreement in the Pearson function as well as
-minimizing the residual.""",
+    group.add_option(
+        '--plot-parameter',
+        metavar='PLOTPARAM',
+        dest='plotparam',
+        help="""Used when both plotting and --multiple are enabled.
+Choose a PLOTPARAM to plot for each morph (i.e. adding --pp=Pearson means the program
+will display a plot of the Pearson correlation coefficient for each morph-target pair).
+PLOTPARAM is not case sensitive, so both Pearson and pearson indicate the same parameter.
+When PLOTPARAM is not specified, Rw values for each morph-target pair will be plotted.
+PLOTPARAM will be displayed as the vertical axis label for the plot.""",
     )
 
     # Manipulations
@@ -222,8 +239,8 @@ def custom_error(self, msg):
     group = optparse.OptionGroup(
         parser, "Plot Options", """These options control plotting.
 The manipulated and target PDFs will be plotted against each other with a
-difference curve below. When --multiple is enabled, a plot of Rw values for
-each file will be shown instead."""
+difference curve below. When --multiple is enabled, the value of a parameter (specified by
+--plot-parameter) will be plotted instead."""
     )
     parser.add_option_group(group)
     group.add_option(
@@ -539,14 +556,30 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True):
         save_fail_message = "Unable to save summary to directory."
         parser.custom_error(save_fail_message)
 
-    # Plot the rw values for each target if requested
-    # FIXME: create functionality to plot other data (scale, stretch, smear, etc.)
+    # Plot the values of some parameter for each target if requested
     if plot_opt:
         plot_results = io.tabulate_results(morph_results)
-        if field_list is not None:
-            pdfplot.plot_rws(field_list, plot_results["Rw"], field)
+        # Default parameter is Rw
+        param_name = r"$R_w$"
+        param_list = plot_results["Rw"]
+        # Find parameter if specified
+        if opts.plotparam is not None:
+            param_name = opts.plotparam
+            param_list = tools.case_insensitive_dictionary_search(opts.plotparam, plot_results)
+        # Not an available parameter to plot or no values found for the parameter
+        if param_list is None:
+            parser.custom_error("Cannot find specified plot parameter. No plot shown.")
         else:
-            pdfplot.plot_rws(target_file_names, plot_results["Rw"])
+            try:
+                if field_list is not None:
+                    pdfplot.plot_param(field_list, param_list, param_name, field)
+                else:
+                    pdfplot.plot_param(target_file_names, param_list, param_name)
+            # Can occur for non-refined plotting parameters
+            # i.e. --smear is not selected as an option, but smear is the plotting parameter
+            except ValueError:
+                parser.custom_error("The plot parameter is missing values for at least one morph and target pair. "
+                                    "No plot shown.")
 
     return morph_results
 
diff --git a/diffpy/pdfmorph/pdfplot.py b/diffpy/pdfmorph/pdfplot.py
@@ -208,13 +208,15 @@ def comparePDFs(
     return
 
 
-def plot_rws(target_labels, rws, field=None):
+def plot_param(target_labels, param_list, param_name=None, field=None):
     """
     Plot Rw values for multiple morphs.
     :param target_labels: Names (or field if --sort-by given) of each file acting as target for the morph.
     :type target_labels: list
-    :param rws: Contains the Rw values corresponding to each file.
-    :type rws: list
+    :param param_list: Contains the values of some parameter corresponding to each file.
+    :type param_list: list
+    :param param_name: Name of the parameter.
+    :type param_name: str
     :param field: When not None and entries in field are numerical, a line chart of Rw versus field is made.
                   When None (default) or values are non-numerical, it plots a bar chart of Rw values per file.
     :type field: list or None
@@ -245,9 +247,10 @@ def plot_rws(target_labels, rws, field=None):
                 numerical = False
 
     if numerical:
-        # Plot Rw vs Temperature
-        plt.plot(target_labels, rws, linestyle='-', marker='o')
-        plt.ylabel(r"$R_w$")
+        # Plot the parameter against a numerical field
+        plt.plot(target_labels, param_list, linestyle='-', marker='o')
+        if param_name is not None:
+            plt.ylabel(rf"{param_name}")
         plt.xlabel(rf"{field}")
         plt.minorticks_on()
 
@@ -263,8 +266,9 @@ def plot_rws(target_labels, rws, field=None):
         plt.xticks(rotation=angle)
 
         # Plot Rw for each file
-        plt.bar(target_labels, rws)
-        plt.ylabel(r"$R_w$")
+        plt.bar(target_labels, param_list)
+        if param_name is not None:
+            plt.ylabel(rf"{param_name}")
         if field is None:
             plt.xlabel(r"Target File")
         else:
diff --git a/diffpy/pdfmorph/tests/test_pdfmorphapp.py b/diffpy/pdfmorph/tests/test_pdfmorphapp.py
@@ -63,6 +63,8 @@ def test_parser_numerical(self, setup_parser):
         assert len(n_args) == 1  # Check one leftover
 
     def test_parser_systemexits(self, setup_parser):
+        # ###Basic tests for any variety of morphing###
+
         # Ensure only two pargs given for morphing
         (opts, pargs) = self.parser.parse_args(["toofewfiles"])
         with pytest.raises(SystemExit):
@@ -80,6 +82,7 @@ def test_parser_systemexits(self, setup_parser):
         with pytest.raises(SystemExit):
             single_morph(self.parser, opts, pargs, stdout_flag=False)
 
+        # ###Tests exclusive to multiple morphs###
         # Make sure we save to a directory that exists (user must create the directory if non-existing)
         (opts, pargs) = self.parser.parse_args([f"{nickel_PDF}", f"{nickel_PDF}", "-s",
                                                 "/nonexisting_directory/no_way_this_exists/nonexisting_path"])
@@ -101,7 +104,17 @@ def test_parser_systemexits(self, setup_parser):
         with pytest.raises(SystemExit):
             multiple_morphs(self.parser, opts, pargs, stdout_flag=False)
         (opts, pargs) = self.parser.parse_args([f"{nickel_PDF}", f"{testsequence_dir}", "--sort-by", "fake_field",
-                                               "--serial-file", f"{serial_JSON}"])
+                                                "--serial-file", f"{serial_JSON}"])
+        with pytest.raises(SystemExit):
+            multiple_morphs(self.parser, opts, pargs, stdout_flag=False)
+
+        # Try plotting an unknown parameter
+        (opts, pargs) = self.parser.parse_args([f"{nickel_PDF}", f"{testsequence_dir}", "--plot-parameter", "unknown"])
+        with pytest.raises(SystemExit):
+            multiple_morphs(self.parser, opts, pargs, stdout_flag=False)
+
+        # Try plotting an unrefined parameter
+        (opts, pargs) = self.parser.parse_args([f"{nickel_PDF}", f"{testsequence_dir}", "--plot-parameter", "stretch"])
         with pytest.raises(SystemExit):
             multiple_morphs(self.parser, opts, pargs, stdout_flag=False)
 
diff --git a/diffpy/pdfmorph/tests/test_pdfmorphio.py b/diffpy/pdfmorph/tests/test_pdfmorphio.py
@@ -51,7 +51,7 @@ def ignore_path(line):
         tmp_succinct_name = tmp_succinct.resolve().as_posix()
 
         (opts, pargs) = self.parser.parse_args(["--multiple", "--sort-by", "temperature", "-s", tmp_succinct_name,
-                                                "-n", "--snf", tssf])
+                                                "-n", "--save-names-file", tssf])
         pargs = [morph_file, testsequence_dir]
         multiple_morphs(self.parser, opts, pargs, stdout_flag=False)
 
@@ -79,7 +79,7 @@ def ignore_path(line):
         tmp_verbose_name = tmp_verbose.resolve().as_posix()
 
         (opts, pargs) = self.parser.parse_args(["--multiple", "--sort-by", "temperature", "-s", tmp_verbose_name,
-                                                "-n", "--snf", tssf, "--verbose"])
+                                                "-n", "--save-names-file", tssf, "--verbose"])
         pargs = [morph_file, testsequence_dir]
         multiple_morphs(self.parser, opts, pargs, stdout_flag=False)
 
