Merge pull request #33 from elmbeech/master

release v4.0.2

Author: elmbeech

README.md

@@ -125,6 +125,9 @@ Developers, please make pull requests to the https://github.com/elmbeech/physice
 + evt generate lineage tree graph output files.
 
 ## Release Notes:
++ version 4.0.2 (2025-06-29): elmbeech/physicelldataloader
+    + minor bugfixes.
+
 + version 4.0.1 (2025-06-24): elmbeech/physicelldataloader
     + man updated.
     + minor bugfixes.

man/TUTORIAL_commandline.md

@@ -9,7 +9,7 @@ The command parameter mimics the related python3 function arguments as closely a
 You can always call the [help](https://en.wikipedia.org/wiki/Help!) parameter ( pcdl\_command -h),
 to access the man page for a pcdl command!
 
-Please spend some time to learn about each of the 18 commands, by studying its man page.
+Please spend some time to learn about each of the about 20 commands, by studying its man page.
 This will truly make you a power user!
 
 

man/TUTORIAL_python3_vtk.md

@@ -2,8 +2,7 @@
 
 [Vtk](https://vtk.org/) the visualization tool kit is a software for image processing, 3D graphics, volume rendering and visualization. \
 Naturally, we will work here with the [vtk](https://pypi.org/project/vtk/) python binding.
-Additionally, we will have a look at [fury](https://fury.gl/latest/index.html),
-a python library for scientific visualization and 3D animations that can read vtk files too.
+Additionally, we will have a look at the [pyvista](https://docs.pyvista.org/) and [fury](https://fury.gl/latest/index.html) python libraries for scientific visualization that can read vtk files too.
 
 
 

pcdl/VERSION.py

@@ -1 +1 @@
-__version__ = '4.0.1'
+__version__ = '4.0.2'

pcdl/commandline.py

@@ -338,7 +338,8 @@ def get_conc_attribute():
         keep = set(args.keep),
         allvalues = b_allvalues,
     )
-    s_opathfile = f'{s_path}/timeseries_conc_attribute_{s_values}.json'
+    s_ofile = f"timeseries_conc_attribute_{s_values.replace(' ','_')}.json"
+    s_opathfile = s_path + '/' + s_ofile
     json.dump(dl_variable, open(s_opathfile, 'w'), sort_keys=True)
     # going home
     return s_opathfile
@@ -1038,7 +1039,7 @@ def get_cell_attribute():
         b_allvalues = True if args.allvalues.lower().startswith('t') else False
         if b_allvalues:
             s_values = 'all'
-        s_opathfile = f"{s_pathfile.replace('.xml','')}_{s_values}.json"
+        s_opathfile = f"{s_pathfile.replace('.xml','')}_{s_values.replace(' ','_')}.json"
 
     else:
         mcdsts = pcdl.TimeSeries(
@@ -1056,7 +1057,8 @@ def get_cell_attribute():
         b_allvalues = True if args.allvalues.lower().startswith('t') else False
         if b_allvalues:
             s_values = 'all'
-        s_opathfile = f'{s_path}/timeseries_cell_attribute_{s_values}.json'
+        s_ofile = f"timeseries_cell_attribute_{s_values.replace(' ','_')}.json"
+        s_opathfile = s_path + '/' + s_ofile
 
     # going home
     dl_variable = mcdsts.get_cell_attribute(
@@ -1375,11 +1377,10 @@ def get_anndata():
         # going home
         if b_collapse :
             s_opathfile = f'{s_path}/timeseries_cell_{args.scale}.h5ad'
-            s_opathfile = f'{s_path}/timeseries_cell_{args.scale.lower()}.h5ad'
             ann_mcdsts.write_h5ad(s_opathfile)
             return s_opathfile
         else:
-            ls_opathfile = [f"{s_path}/{s_xmlfile.replace('.xml', '_cell_{}.h5ad'.format(args.scale.lower()))}" for s_xmlfile in mcdsts.get_xmlfile_list()]
+            ls_opathfile = [f"{s_path}/{s_xmlfile.replace('.xml', '_cell_{}.h5ad'.format(args.scale))}" for s_xmlfile in mcdsts.get_xmlfile_list()]
             for i, ann_mcds in enumerate(ann_mcdsts):
                 ann_mcds.write_h5ad(ls_opathfile[i])
             return ls_opathfile
@@ -1765,8 +1766,8 @@ def plot_scatter():
             figbgcolor = None if (args.figbgcolor.lower() == 'none') else args.figbgcolor,
         )
         # going home
-        s_opathfile = '/'.join(ls_opathfile[0].split('/')[:-1])
-        return s_opathfile
+        s_opath = '/'.join(ls_opathfile[0].split('/')[:-1])
+        return s_opath
 
 
 def make_cell_vtk():

pcdl/timeseries.py

@@ -80,14 +80,15 @@ def make_gif(path, interface='jpeg'):
     if path.endswith('/'): path = path[:-1]
     if not os.path.isdir(path):
         sys.exit(f'Error @ make_gif : {path} path does not exist.')
-    s_file = path.split('/')[-1]
-    if s_file.startswith('.'): s_file = s_file[1:]
-    if (len(s_file) == 0): s_file = 'movie'
-    s_file += f'_{interface}.gif'
-    s_opathfile = f'{path}/{s_file}'
+    s_ofile = path.split('/')[-1]
+    if s_ofile.startswith('.'): s_ofile = s_ofile[1:]
+    if (len(s_ofile) == 0): s_ofile = 'movie'
+    s_ofile += f'_{interface}.gif'
+    s_ofile = s_ofile.replace(' ','_')
+    s_opathfile = path + '/' + s_ofile
     s_ipathfiles = f'{path}/*.{interface}'
     # genaerate gif
-    s_cmd = f'{s_magick}convert {s_ipathfiles} {s_opathfile}'
+    s_cmd = f'{s_magick}convert "{s_ipathfiles}" "{s_opathfile}"'
     if (os.system(s_cmd) != 0):
         sys.exit("Error @ make_gif : imagemagick could not generatet the gif.")
 
@@ -133,6 +134,7 @@ def make_movie(path, interface='jpeg', framerate=12):
     if s_ofile.startswith('.'): s_ofile = s_ofile[1:]
     if (len(s_ofile) == 0): s_ofile = 'movie'
     s_ofile += f'_{interface}{framerate}.mp4'
+    s_ofile = s_ofile.replace(' ','_')
     s_opathfile = f'{s_path}/{s_ofile}'
 
     # generate input file list
@@ -144,7 +146,7 @@ def make_movie(path, interface='jpeg', framerate=12):
     f.close()
 
     # genearete movie
-    s_cmd = f'ffmpeg -y -r {framerate} -f concat -i ffmpeginput.txt -vcodec libx264 -pix_fmt yuv420p -strict -2 -tune animation -crf 15 -acodec none {s_ofile}'  # -safe 0
+    s_cmd = f'ffmpeg -y -r {framerate} -f concat -i ffmpeginput.txt -vcodec libx264 -pix_fmt yuv420p -strict -2 -tune animation -crf 15 -acodec none "{s_ofile}"'  # -safe 0
     if (os.system(s_cmd) != 0):
         sys.exit("Error @ make_movie : ffmpeg could not generatet the movie.")
     os.remove('ffmpeginput.txt')
@@ -1100,7 +1102,7 @@ def make_ome_tiff(self, cell_attribute='ID', conc_cutoff={}, focus=None, file=Tr
                 s_channel += f'_{s_celltype}'
             if len(ls_celltype) > 0:
                 s_channel += f'_{cell_attribute}'
-            s_tifffile = f'timeseries{s_channel}.ome.tiff'
+            s_tifffile = f"timeseries{s_channel.replace(' ','_')}.ome.tiff"
             if (len(s_tifffile) > 255):
                 print(f"Warning: filename {len(s_tifffile)} > 255 character.")
                 s_tifffile = 'timeseries_channels.ome.tiff'
@@ -1396,9 +1398,10 @@ def plot_timeseries(self, focus_cat=None, focus_num=None, aggregate_num=np.nanme
             return fig
         else:
             if (focus_num == 'count'):
-                s_pathfile = self.path + f'/timeseries_{frame}_{focus_cat}_{focus_num}.{ext}'
+                s_ofile = 'timeseries_{frame}_{focus_cat}_{focus_num}.{ext}'.replace(' ','_')
             else:
-                s_pathfile = self.path + f"/timeseries_{frame}_{focus_cat}_{focus_num}_{aggregate_num.__name__.replace('np.nan','')}.{ext}"
+                s_ofile = f"timeseries_{frame}_{focus_cat}_{focus_num}_{aggregate_num.__name__.replace('np.nan','')}.{ext}".replace(' ','_')
+            s_pathfile = self.path + '/' + s_ofile
             if figbgcolor is None:
                 figbgcolor = 'auto'
             plt.tight_layout()

pcdl/timestep.py

@@ -1300,9 +1300,9 @@ def plot_contour(self, focus, z_slice=0.0, vmin=None, vmax=None, alpha=1, fill=T
 
         else:
             # handle output path and filename
-            s_path = self.path + f'/conc_{focus}_z{round(z_slice,9)}/'
+            s_path = self.path + f"/conc_{focus.replace(' ','_')}_z{round(z_slice,9)}/"
             os.makedirs(s_path, exist_ok=True)
-            s_file = self.xmlfile.replace('.xml', f'_{focus}.{ext}')
+            s_file = self.xmlfile.replace('.xml', f"_{focus.replace(' ','_')}.{ext}")
             s_pathfile = f'{s_path}{s_file}'
             # handle figure background color
             if figbgcolor is None:
@@ -1755,9 +1755,9 @@ def plot_scatter(self, focus='cell_type', z_slice=0.0, z_axis=None, alpha=1, cma
 
         else:
             # handle output path and filename
-            s_path = self.path + f'/cell_{focus}_z{round(z_slice,9)}/'
+            s_path = self.path + f"/cell_{focus.replace(' ','_')}_z{round(z_slice,9)}/"
             os.makedirs(s_path, exist_ok=True)
-            s_file = self.xmlfile.replace('.xml', f'_{focus}.{ext}')
+            s_file = self.xmlfile.replace('.xml', f"_{focus.replace(' ','_')}.{ext}")
             s_pathfile = f'{s_path}{s_file}'
             # handle figure background color
             if figbgcolor is None:
@@ -2087,6 +2087,7 @@ def make_ome_tiff(self, cell_attribute='ID', conc_cutoff={}, focus=None, file=Tr
             if len(ls_celltype) > 0:
                 s_channel += f'_{cell_attribute}'
             s_tifffile = self.xmlfile.replace('.xml', f'{s_channel}.ome.tiff')
+            s_tifffile = s_tifffile.replace(' ','_')
             if (len(s_tifffile) > 255):
                 print(f"Warning: filename {len(s_tifffile)} > 255 character.")
                 s_tifffile = self.xmlfile.replace('.xml', f'_channels.ome.tiff')
@@ -2398,7 +2399,7 @@ def _read_xml(self, xmlfile, output_path='.'):
                 # <cell_definition>
                 s_id = str(x_celltype.get('ID'))
                 # I don't like spaces in cell type names!
-                s_celltype = x_celltype.get('name') #.replace(' ', '_') # ROH
+                s_celltype = x_celltype.get('name') #.replace(' ','_') # ROH
                 d_mcds['cell']['ds_celltype'].update({s_id : s_celltype})
             b_celltype = True
 
@@ -2575,7 +2576,7 @@ def _read_xml(self, xmlfile, output_path='.'):
             # substrate loop
             for i_s, x_substrate in enumerate(x_microenv.find('variables').findall('variable')):
                 # i don't like spaces in species names!
-                s_substrate = x_substrate.get('name') #.replace(' ', '_') # ROH
+                s_substrate = x_substrate.get('name') #.replace(' ','_') # ROH
 
                 d_mcds['raw_substrate'][s_substrate] = {}
                 d_mcds['raw_substrate'][s_substrate]['units'] = x_substrate.get('units')
@@ -2693,7 +2694,7 @@ def _read_xml(self, xmlfile, output_path='.'):
             for x_celltype in x_celldata.find('cell_types').findall('type'):
                 s_id = str(x_celltype.get('ID'))
                 # I don't like spaces in cell type names!
-                s_celltype = x_celltype.text #.replace(' ', '_')  # ROH
+                s_celltype = x_celltype.text #.replace(' ','_')  # ROH
                 d_mcds['cell']['ds_celltype'].update({s_id : s_celltype})
             b_celltype = True
         except AttributeError:
@@ -2703,7 +2704,7 @@ def _read_xml(self, xmlfile, output_path='.'):
         if not b_celltype:
             for x_label in x_celldata.find('labels').findall('label'):
                 # I don't like spaces in cell type names!
-                s_variable = x_label.tex #.replace(' ', '_')  # ROH
+                s_variable = x_label.tex #.replace(' ','_')  # ROH
                 if s_variable in es_var_cell:
                     for i_id in range(int(x_label.get('size'))):
                         s_id = str(i_id)
@@ -2714,7 +2715,7 @@ def _read_xml(self, xmlfile, output_path='.'):
         ls_variable = []
         for x_label in x_celldata.find('labels').findall('label'):
             # I don't like spaces in my dictionary keys!
-            s_variable = x_label.text #.replace(' ', '_')  # ROH
+            s_variable = x_label.text #.replace(' ','_')  # ROH
             i_variable = int(x_label.get('size'))
             s_unit = x_label.get('units')