Font embedding on PDFs

* New option to force usage of type 42 fonts in PDFs
* MatPlotLib will insert the appropriate font glyphs into the document, aka subsetting
* Updated header documentations
* Updated command line options

KaSaAn/scripts/kappa_catalytic_potential.py

@@ -4,14 +4,15 @@
 
 ``` {.text}
 usage: kappa_catalytic_potential [-h] [-d DIRECTORY] -e ENZYME_NAME -s SUBSTRATE_NAME [-v] [-o OUTPUT_FILE] [-p SNAPSHOT_PATTERN] [-ts TEXT_SIZE]
-[-h]                Show detailed help.
-[-d DIRECTORY]      Directory containing the snapshots.
--e ENZYME_NAME      Name of the first agent.
--s SUBSTRATE_NAME   Name of the second agent.
-[-v]                If set, print additional information to standard output.
-[-o OUTPUT_FILE]    If specified, save to file; else print to standard output.
--p SNAPSHOT_PREFIX  The prefix by which the snapshots are named.
-[-ts TEXT_SIZE]     Override default size for text, in points.
+[-h]                            Show detailed help.
+[-d DIRECTORY]                  Directory containing the snapshots.
+-e ENZYME_NAME                  Name of the first agent.
+-s SUBSTRATE_NAME               Name of the second agent.
+[-v]                            If set, print additional information to standard output.
+[-o OUTPUT_FILE]                If specified, save to file; else print to standard output.
+-p SNAPSHOT_PREFIX              The prefix by which the snapshots are named.
+[-ts TEXT_SIZE]                 Override default size for text, in points.
+[--text_instead_of_paths]       Output text elements instead of paths; embeds used glyphs
 ```
 """
 
@@ -50,10 +51,15 @@ def main(args=None):
                         help='Pattern by which the snapshots are named; e.g. <snap_4.ka> would have <snap_*.ka>.')
     parser.add_argument('-ts', '--text_size', type=int,
                         help="If given, set point size for all text elements, overriding MatPlotLib's default.")
+    parser.add_argument('--text_instead_of_paths', action='store_true',
+                        help='If set, figure will embed used glyphs and export text elements, instead of rendering the'
+                             ' glyphs into paths. Only supported for PDF export.')
 
     args = parser.parse_args()
     if args.text_size:
         mpl.rcParams['font.size'] = args.text_size
+    if args.text_instead_of_paths:
+        plt.rcParams['pdf.fonttype'] = 42
 
     data = get_potential_of_folder(args.directory, args.enzyme_name, args.substrate_name,
                                    args.verbose, args.snapshot_pattern)

KaSaAn/scripts/kappa_contact_map.py

@@ -12,6 +12,7 @@
 [--summarize_flagpole]      Summarizes state-only sites as a numeric annotation.
 [--keep_axes_ticks]         Show the X & Y axes ticks.
 [-ts TEXT_SIZE]             Override default size for text, in points.
+[--text_instead_of_paths]   Output text elements instead of paths; embeds used glyphs
 ```
 """
 
@@ -58,10 +59,15 @@ def main():
                         ' for manual agent placement.')
     parser.add_argument('-ts', '--text_size', type=int,
                         help="If given, set point size for all text elements, overriding MatPlotLib's default.")
+    parser.add_argument('--text_instead_of_paths', action='store_true',
+                        help='If set, figure will embed used glyphs and export text elements, instead of rendering the'
+                             ' glyphs into paths. Only supported for PDF export.')
     args = parser.parse_args()
 
     if args.text_size:
         mpl.rcParams['font.size'] = args.text_size
+    if args.text_instead_of_paths:
+        plt.rcParams['pdf.fonttype'] = 42
 
     this_cm = KappaContactMap(args.input_file_name)
     fig, ax = plt.subplots(figsize=args.fig_size, layout='constrained')

KaSaAn/scripts/kappa_observable_coplotter.py

@@ -27,6 +27,7 @@
                                     outside left upper, outside right upper,
                                     outside left lower, outside right lower
 [--legend_ncol LEGEND_NCOL]     Number of columns for the legend.
+[--text_instead_of_paths]       Output text elements instead of paths; embeds used glyphs
 ```
 """
 
@@ -88,10 +89,15 @@ def main():
                         help='Number of columns for the legend.')
     parser.add_argument('-ts', '--text_size', type=int,
                         help="If given, set point size for all text elements, overriding MatPlotLib's default.")
+    parser.add_argument('--text_instead_of_paths', action='store_true',
+                        help='If set, figure will embed used glyphs and export text elements, instead of rendering the'
+                             ' glyphs into paths. Only supported for PDF export.')
     args = parser.parse_args()
 
     if args.text_size:
         mpl.rcParams['font.size'] = args.text_size
+    if args.text_instead_of_paths:
+        plt.rcParams['pdf.fonttype'] = 42
 
     fig, ax = plt.subplots(figsize=args.figure_size, layout='constrained')
     observable_coplot_axis_annotator(target_axis=ax,

KaSaAn/scripts/kappa_observable_plotter.py

@@ -27,6 +27,7 @@
                                     outside left upper, outside right upper,
                                     outside left lower, outside right lower
 [--legend_ncol LEGEND_NCOL]     Number of columns for the legend.
+[--text_instead_of_paths]       Output text elements instead of paths; embeds used glyphs
 ```
 """
 
@@ -91,10 +92,15 @@ def main():
                         help='Override location of the legend. Options prefixed with <outside> plot outside the axes.')
     parser.add_argument('--legend_ncol', type=int, default=1,
                         help='Number of columns for the legend.')
+    parser.add_argument('--text_instead_of_paths', action='store_true',
+                        help='If set, figure will embed used glyphs and export text elements, instead of rendering the'
+                             ' glyphs into paths. Only supported for PDF export.')
     args = parser.parse_args()
 
     if args.text_size:
         mpl.rcParams['font.size'] = args.text_size
+    if args.text_instead_of_paths:
+        plt.rcParams['pdf.fonttype'] = 42
 
     this_data = observable_file_reader(args.input_file_name)
 

KaSaAn/scripts/kappa_snapshot_largest_complex_time.py

@@ -4,36 +4,38 @@
 
 ``` {.text}
 usage: kappa_snapshot_largest_complex_time [-h] [-d DIRECTORY] [-p PATTERN] [-cs COLORING_SCHEME] [-o OUTPUT_NAME] [-fs WIDTH HEIGHT] [--lin_log] [--log_lin] [--log_log] [--un_stacked] [-mt MULTI_THREAD] [-ts TEXT_SIZE]
-[-h]                    Show detailed help.
-[-d DIRECTORY]          Directory where snapshots are stored, default is <.>
-[-p PATTERN]            Pattern that groups desired snapshots names; default 'snap*.ka'.
-[-cs FILE]              Optional file containing a dictionary with color scheme to use for species composition. E.g.
-                        <{"Bob": #fff, "Mary": #999, "Sue": #222}>, where the color can be anything converable to a
-                        color by MatPlotLib (e.g. RGB[A] tuples, hex-strings, XKCD colors...). Supports KappaAgents,
-                        with or without agent signature, as well as KappaComplexes. If not provided, the sum formula
-                        will be displayed (arbitrary colors per agent, discarding agent signature).
-[-o OUTPUT_NAME]        The common file name for saving figures; shown if not given.
-[-fs WIDTH HEIGHT]      Size of the resulting figure, in inches.
-[--lin_log]             If specified, produce an additional plot with linear X-axis and logarithmic Y-axis.
-[--log_lin]             If specified, produce an additional plot with logarithmic X-axis and linear Y-axis.
-[--log_log]             If specified, produce an additional plot with logarithmic X-axis and logarithmic Y-axis.
-[--un_stacked]          If given, produce regular non-stacked plot.
-[--mt THREADS]          Launch multiple threads for reading snapshots. Safe, but always less performant: WIP.
-[-ts TEXT_SIZE]         Override default size for text, in points.
-[--stack_method] {...}  The order of elements in the stackplot. Choices are:
-                        first_in_first_out:     Patterns are plotted in the order in which they are encountered while reading snapshots.
-                        interleaved_initial:    Patterns are plotted alternating large and small abundances, as measured in the first snapshot.
-                        interleaved_final:      Patterns are plotted alternating large and small abundances, as measured in the final snapshot.
-                        ascending_initial:      Patterns are plotted in ascending abundances, as measured in the first snapshot.
-                        ascending_final:        Patterns are plotted in ascending abundances, as measured in the final snapshot.
-                        descending_initial:     Patterns are plotted in descending abundances, as measured in the first snapshot.
-                        descending_final:       Patterns are plotted in descending abundances, as measured in the final snapshot.
+[-h]                        Show detailed help.
+[-d DIRECTORY]              Directory where snapshots are stored, default is <.>
+[-p PATTERN]                Pattern that groups desired snapshots names; default 'snap*.ka'.
+[-cs FILE]                  Optional file containing a dictionary with color scheme to use for species composition. E.g.
+                            <{"Bob": #fff, "Mary": #999, "Sue": #222}>, where the color can be anything converable to a
+                            color by MatPlotLib (e.g. RGB[A] tuples, hex-strings, XKCD colors...). Supports KappaAgents,
+                            with or without agent signature, as well as KappaComplexes. If not provided, the sum formula
+                            will be displayed (arbitrary colors per agent, discarding agent signature).
+[-o OUTPUT_NAME]            The common file name for saving figures; shown if not given.
+[-fs WIDTH HEIGHT]          Size of the resulting figure, in inches.
+[--lin_log]                 If specified, produce an additional plot with linear X-axis and logarithmic Y-axis.
+[--log_lin]                 If specified, produce an additional plot with logarithmic X-axis and linear Y-axis.
+[--log_log]                 If specified, produce an additional plot with logarithmic X-axis and logarithmic Y-axis.
+[--un_stacked]              If given, produce regular non-stacked plot.
+[--mt THREADS]              Launch multiple threads for reading snapshots. Safe, but always less performant: WIP.
+[-ts TEXT_SIZE]             Override default size for text, in points.
+[--stack_method] {...}      The order of elements in the stackplot. Choices are:
+                                first_in_first_out:     Patterns are plotted in the order in which they are encountered while reading snapshots.
+                                interleaved_initial:    Patterns are plotted alternating large and small abundances, as measured in the first snapshot.
+                                interleaved_final:      Patterns are plotted alternating large and small abundances, as measured in the final snapshot.
+                                ascending_initial:      Patterns are plotted in ascending abundances, as measured in the first snapshot.
+                                ascending_final:        Patterns are plotted in ascending abundances, as measured in the final snapshot.
+                                descending_initial:     Patterns are plotted in descending abundances, as measured in the first snapshot.
+                                descending_final:       Patterns are plotted in descending abundances, as measured in the final snapshot.
+[--text_instead_of_paths]   Output text elements instead of paths; embeds used glyphs
 ```
 """
 
 import argparse
 import ast
 import matplotlib as mpl
+import matplotlib.colors as mpco
 import matplotlib.pyplot as plt
 from pathlib import Path
 from KaSaAn.core.KappaError import ComplexParseError, AgentParseError
@@ -83,12 +85,17 @@ def main():
                         ' 1, so a single-threaded for-loop.')
     parser.add_argument('-ts', '--text_size', type=int,
                         help="If given, set point size for all text elements, overriding MatPlotLib's default.")
-    parser.add_argument('--stack_method', choices=_stacked_plot_methods.keys(), type=str,
+    parser.add_argument('--stack_method', choices=_stacked_plot_methods.keys(), type=str, default=next(iter(_stacked_plot_methods)),
                         help='\n'.join(['{}:\t{}'.format(k, v) for k, v in _stacked_plot_methods.items()]))
+    parser.add_argument('--text_instead_of_paths', action='store_true',
+                        help='If set, figure will embed used glyphs and export text elements, instead of rendering the'
+                             ' glyphs into paths. Only supported for PDF export.')
     args = parser.parse_args()
 
     if args.text_size:
         mpl.rcParams['font.size'] = args.text_size
+    if args.text_instead_of_paths:
+        plt.rcParams['pdf.fonttype'] = 42
 
     # for user-defined coloring schemes, read the dictionary from a file, convert keys
     # Since single-agents can be interpreted as KappaComplexes, and that preserves sorting & comparisons, we cast
@@ -98,11 +105,15 @@ def main():
         with open(args.coloring_scheme, 'r') as cs_file:
             coloring_scheme_raw = ast.literal_eval(cs_file.read())
             for key, value in coloring_scheme_raw.items():
+                if mpco.is_color_like(value):
+                    this_color = value
+                else:
+                    this_color = mpco.to_hex(eval(value))
                 try:
-                    coloring_scheme[KappaAgent(key)] = value
+                    coloring_scheme[KappaAgent(key)] = this_color
                 except AgentParseError:
                     try:
-                        coloring_scheme[KappaComplex(key)] = value
+                        coloring_scheme[KappaComplex(key)] = this_color
                     except ComplexParseError:
                         raise ValueError('Could not parse {} as a KappaComplex nor a KappaAgent'.format(key))
     else:

KaSaAn/scripts/kappa_snapshot_visualizer_network.py

@@ -4,15 +4,16 @@
 
 ``` {.text}
 usage: kappa_snapshot_visualizer_network [-h] -sf SNAPSHOT_FILE_NAME [-cs COLORING_SCHEME] [-p [HIGHLIGHT_PATTERNS ...]] [-of OUTPUT_FILE] [-fs WIDTH HEIGHT] [-ns NODE_SIZE] [-ew EDGE_WIDTH] [-ts TEXT_SIZE]
-[-h]                        Show detailed help.
--sf SNAPSHOT_FILE_NAME      Name of the snapshot file to be viewed.
-[-cs FILE_NAME]             Optional file containing an agent coloring scheme.
-[-p [...]]                  Agent patterns to highlight.
-[-of OUTPUT_FILE]           The common file name for saving figures; shown if not given.
-[-fs WIDTH HEIGHT]          Size of the resulting figure, in inches.
-[-ns NODE_SIZE]             Size of nodes; default of 300 as used by NetworkX.
-[-ew EDGE_WIDTH]            Width of edges; default of 1.0 as used by NetworkX.
-[-ts TEXT_SIZE]             Override default size for text, in points.
+[-h]                            Show detailed help.
+-sf SNAPSHOT_FILE_NAME          Name of the snapshot file to be viewed.
+[-cs FILE_NAME]                 Optional file containing an agent coloring scheme.
+[-p [...]]                      Agent patterns to highlight.
+[-of OUTPUT_FILE]               The common file name for saving figures; shown if not given.
+[-fs WIDTH HEIGHT]              Size of the resulting figure, in inches.
+[-ns NODE_SIZE]                 Size of nodes; default of 300 as used by NetworkX.
+[-ew EDGE_WIDTH]                Width of edges; default of 1.0 as used by NetworkX.
+[-ts TEXT_SIZE]                 Override default size for text, in points.
+[--text_instead_of_paths]       Output text elements instead of paths; embeds used glyphs
 ```
 
 The following are two views of the same snapshot, one showing all nodes, the other
@@ -66,11 +67,16 @@ def main():
                         help='Width of edges; default of 1.0 as used by NetworkX.')
     parser.add_argument('-ts', '--text_size', type=int,
                         help="If given, set point size for all text elements, overriding MatPlotLib's default.")
+    parser.add_argument('--text_instead_of_paths', action='store_true',
+                        help='If set, figure will embed used glyphs and export text elements, instead of rendering the'
+                             ' glyphs into paths. Only supported for PDF export.')
 
     args = parser.parse_args()
 
     if args.text_size:
         mpl.rcParams['font.size'] = args.text_size
+    if args.text_instead_of_paths:
+        plt.rcParams['pdf.fonttype'] = 42
 
     # render graph
     figure_list = render_snapshot_as_plain_graph(snapshot_file_name=args.snapshot_file_name,

KaSaAn/scripts/kappa_snapshot_visualizer_patchwork.py

@@ -4,14 +4,15 @@
 
 ``` {.text}
 usage: kappa_snapshot_visualizer_patchwork [-h] -sf SNAPSHOT_FILE [-cs COLORING_SCHEME] [-vm {all,mass,count,size}] [-of OUTPUT_FILE] [-fs WIDTH HEIGHT] [-dpi DOTS_PER_INCH] [-ts TEXT_SIZE]
-[-h]                        Show detailed help.
--sf SNAPSHOT_FILE_NAME      Name of snapshot to visualize.
-[-cs FILE_NAME]             File specifying a coloring scheme.
-[-vm [all|mass|count|size]] How to scale area; default plots all three.
-[-of OUTPUT_FILE]           The common file name for saving figures; shown if not given.
-[-fs WIDTH HEIGHT]          Size of the resulting figure, in inches.
-[-dpi DOTS_PER_INCH]        Resolution of the figure.
-[-ts TEXT_SIZE]             Override default size for text, in points.
+[-h]                            Show detailed help.
+-sf SNAPSHOT_FILE_NAME          Name of snapshot to visualize.
+[-cs FILE_NAME]                 File specifying a coloring scheme.
+[-vm [all|mass|count|size]]     How to scale area; default plots all three.
+[-of OUTPUT_FILE]               The common file name for saving figures; shown if not given.
+[-fs WIDTH HEIGHT]              Size of the resulting figure, in inches.
+[-dpi DOTS_PER_INCH]            Resolution of the figure.
+[-ts TEXT_SIZE]                 Override default size for text, in points.
+[--text_instead_of_paths]       Output text elements instead of paths; embeds used glyphs
 ```
 
 For example:
@@ -63,11 +64,16 @@ def main(args=None):
                         help='Resolution of the figure, specified as dots per inch.')
     parser.add_argument('-ts', '--text_size', type=int,
                         help="If given, set point size for all text elements, overriding MatPlotLib's default.")
+    parser.add_argument('--text_instead_of_paths', action='store_true',
+                        help='If set, figure will embed used glyphs and export text elements, instead of rendering the'
+                             ' glyphs into paths. Only supported for PDF export.')
 
     args = parser.parse_args()
 
     if args.text_size:
         mpl.rcParams['font.size'] = args.text_size
+    if args.text_instead_of_paths:
+        plt.rcParams['pdf.fonttype'] = 42
 
     # for user-defined coloring schemes, read the dictionary from a file, convert keys to KappaAgent
     if args.coloring_scheme: