Merge pull request #217 from PhysiCell-Tools/development

Development

Author: rheiland

VERSION.txt

@@ -1 +1 @@
-2.37.8
+2.37.9

bin/biwt_dev.py

@@ -0,0 +1,34 @@
+import os
+def biwt_dev_mode(biwt):
+    BIWT_SPATIAL_DEV = os.getenv('BIWT_SPATIAL_DEV', 'False')
+    BIWT_SPATIAL_DEV = BIWT_SPATIAL_DEV=='True'
+    if BIWT_SPATIAL_DEV:
+        # file_name = "./data/visium_adata.h5ad"
+        # file_name = "./data/Zhuang-ABCA-1-1.064_raw_wClusterAnnots.h5ad"
+        file_name = "./data/abc/metadata/Zhuang-ABCA-1/20231215/views/cell_metadata_with_cluster_annotation.csv"
+        if "Zhuang" in file_name:
+            biwt.column_line_edit.setText("subclass")
+        else:
+            biwt.column_line_edit.setText("cluster")
+        biwt.import_file(file_name)
+        # biwt.continue_from_import()
+        # biwt.window.process_window() # process spatial y/n window
+        # biwt.window.process_window() # process edit window
+        # biwt.window.process_window() # process rename window
+        # biwt.continue_from_spatial_query()
+        # biwt.continue_from_edit()
+        # biwt.window.process_window() # process rename window
+        # biwt.set_cell_positions()
+        # biwt.import_file("./data/visium_adata.h5ad")
+        # biwt.continue_from_import()
+        # biwt.continue_from_spatial_query()
+        # biwt.continue_from_edit()
+        # biwt.window.process_window() # process rename window
+        # biwt.set_cell_positions()
+    else:
+        biwt.import_file("./data/pbmc3k_clustered.h5ad")
+        biwt.continue_from_edit()
+        biwt.window.process_window() # process rename window
+        biwt.window.process_window() # process cell count window
+        # biwt.continue_from_rename()
+        # biwt.set_cell_positions()

bin/bioinf_import_tab.py bin/biwt_tab.pybin/bioinf_import_tab.py renamed to bin/biwt_tab.py

@@ -530,7 +530,7 @@ def new_cell_def(self):
             else:
                 break
 
-        self.new_cell_def_named(cdname) # added by DRB to make it easier for BioinfImport to add a new cell type programmatically
+        self.new_cell_def_named(cdname) # added by DRB to make it easier for BIWT to add a new cell type programmatically
 
     def new_cell_def_named(self, cdname):
 

bin/cell_def_tab.py

@@ -30,7 +30,7 @@
 from PyQt5.QtGui import QPixmap
 
 from studio_classes import QHLine
-from bioinf_import_tab import BioinfImport
+from biwt_tab import BioinformaticsWalkthrough
 
 import numpy as np
 import matplotlib
@@ -66,7 +66,7 @@ def __init__(self,name):
 
 class ICs(QWidget):
 
-    def __init__(self, config_tab, celldef_tab, bioinf_import_flag, bioinf_import_test, bioinf_import_test_spatial):
+    def __init__(self, config_tab, celldef_tab, biwt_flag):
         super().__init__()
         # global self.config_params
 
@@ -75,7 +75,7 @@ def __init__(self, config_tab, celldef_tab, bioinf_import_flag, bioinf_import_te
         self.celldef_tab = celldef_tab
         self.config_tab = config_tab
 
-        self.bioinf_import_flag = bioinf_import_flag
+        self.biwt_flag = biwt_flag
 
         # self.circle_radius = 100  # will be set in run_tab.py using the .xml
         # self.mech_voxel_size = 30
@@ -186,9 +186,9 @@ def __init__(self, config_tab, celldef_tab, bioinf_import_flag, bioinf_import_te
 
         self.tab_widget = QTabWidget()
         self.base_tab_id = self.tab_widget.addTab(self.create_base_ics_tab(),"Base")
-        if self.bioinf_import_flag:
-            self.bioinf_import_tab = BioinfImport(self.config_tab, self.celldef_tab, self, bioinf_import_test, bioinf_import_test_spatial)
-            self.tab_widget.addTab(self.bioinf_import_tab,"Bioinformatics Import")
+        if self.biwt_flag:
+            self.biwt_tab = BioinformaticsWalkthrough(self.config_tab, self.celldef_tab, self)
+            self.tab_widget.addTab(self.biwt_tab,"BIWT")
 
         self.layout = QVBoxLayout(self)
         self.layout.addWidget(self.tab_widget)
@@ -1943,8 +1943,8 @@ def import_from_file(self, full_path_rules_name):
     def fill_gui(self):
         self.csv_folder.setText(self.config_tab.csv_folder.text())
         self.output_file.setText(self.config_tab.csv_file.text())
-        if self.bioinf_import_flag:
-            self.bioinf_import_tab.fill_gui()
+        if self.biwt_flag:
+            self.biwt_tab.fill_gui()
 
     def on_enter_axes(self, event):
         self.mouse_on_axes = True
@@ -1966,4 +1966,3 @@ def mouseMoved(self, event):
         self.ax0.set_title(f"(x,y) = ({round(current_location[0])}, {round(current_location[1])})")
         self.canvas.update()
         self.canvas.draw()
-

bin/ics_tab.py

@@ -80,7 +80,7 @@ def quit_cb():
     studio_app.quit()
 
 class PhysiCellXMLCreator(QWidget):
-    def __init__(self, config_file, studio_flag, skip_validate_flag, rules_flag, model3D_flag, tensor_flag, exec_file, nanohub_flag, is_movable_flag, pytest_flag, bioinf_import_flag, bioinf_import_test_flag, bioinf_import_test_spatial_flag, parent = None):
+    def __init__(self, config_file, studio_flag, skip_validate_flag, rules_flag, model3D_flag, tensor_flag, exec_file, nanohub_flag, is_movable_flag, pytest_flag, biwt_flag, parent = None):
         super(PhysiCellXMLCreator, self).__init__(parent)
         if model3D_flag:
             try:
@@ -106,7 +106,7 @@ def __init__(self, config_file, studio_flag, skip_validate_flag, rules_flag, mod
         self.nanohub_flag = nanohub_flag 
         self.ecm_flag = False 
         self.pytest_flag = pytest_flag 
-        self.bioinf_import_flag = bioinf_import_flag
+        self.biwt_flag = biwt_flag
         print("PhysiCellXMLCreator(): self.nanohub_flag= ",self.nanohub_flag)
 
         self.rules_tab_index = None
@@ -326,7 +326,7 @@ def __init__(self, config_file, studio_flag, skip_validate_flag, rules_flag, mod
 
         if self.studio_flag:
             logging.debug(f'studio.py: creating ICs, Run, and Plot tabs')
-            self.ics_tab = ICs(self.config_tab, self.celldef_tab, self.bioinf_import_flag, bioinf_import_test_flag, bioinf_import_test_spatial_flag)
+            self.ics_tab = ICs(self.config_tab, self.celldef_tab, self.biwt_flag)
             self.ics_tab.fill_celltype_combobox()
             self.ics_tab.reset_info()
 
@@ -1362,9 +1362,7 @@ def main():
     nanohub_flag = False
     is_movable_flag = False
     pytest_flag = False
-    bioinf_import_flag = False
-    bioinf_import_test_flag = False
-    bioinf_import_test_spatial_flag = False
+    biwt_flag = False
     try:
         parser = argparse.ArgumentParser(description='PhysiCell Studio.')
 
@@ -1378,9 +1376,7 @@ def main():
         parser.add_argument("-c ", "--config", type=str, help="config file (.xml)")
         parser.add_argument("-e ", "--exec", type=str, help="executable model")
         # parser.add_argument("-p ", "--pconfig", help="use config/PhysiCell_settings.xml", action="store_true")
-        parser.add_argument("--bioinf_import", help="display bioinformatics import tab on ICs tab", action="store_true")
-        parser.add_argument("--bioinf_import_test", help="immediately start loading anndata w/o spatial", action="store_true")
-        parser.add_argument("--bioinf_import_test_spatial", help="immediately start loading spatial anndata", action="store_true")
+        parser.add_argument("--bioinf_import","--biwt", dest="biwt_flag", help="display bioinformatics walkthrough tab on ICs tab", action="store_true")
         if platform.system() == "Windows":
             exec_file = 'project.exe'
         else:
@@ -1453,12 +1449,8 @@ def main():
         #     else:
         #         print("config_file is NOT valid: ", config_file)
         #         sys.exit()
-        if args.bioinf_import:
-            bioinf_import_flag = True
-        if args.bioinf_import_test:
-            bioinf_import_test_flag = True
-        if args.bioinf_import_test_spatial:
-            bioinf_import_test_spatial_flag = True
+        if args.biwt_flag:
+            biwt_flag = True
     except:
         # print("Error parsing command line args.")
         sys.exit(-1)
@@ -1539,7 +1531,8 @@ def main():
             # print("Warning: Rules module not found.\n")
 
     # print("calling PhysiCellXMLCreator with rules_flag= ",rules_flag)
-    ex = PhysiCellXMLCreator(config_file, studio_flag, skip_validate_flag, rules_flag, model3D_flag, tensor_flag, exec_file, nanohub_flag, is_movable_flag, pytest_flag, bioinf_import_flag, bioinf_import_test_flag, bioinf_import_test_spatial_flag)
+    ex = PhysiCellXMLCreator(config_file, studio_flag, skip_validate_flag, rules_flag, model3D_flag, tensor_flag, exec_file, nanohub_flag, is_movable_flag, pytest_flag, biwt_flag
+                             )
     print("size=",ex.size())  # = PyQt5.QtCore.QSize(1100, 770)
     # ex.setFixedWidth(1101)  # = PyQt5.QtCore.QSize(1100, 770)
     # print("width=",ex.size())

bin/studio.py

@@ -78,7 +78,7 @@ def quit_cb():
 
 
 class PhysiCellXMLCreator(QWidget):
-    def __init__(self, config_file, studio_flag, skip_validate_flag, rules_flag, model3D_flag, tensor_flag, exec_file, nanohub_flag, is_movable_flag, ecm_flag, pytest_flag, parent = None):
+    def __init__(self, config_file, studio_flag, skip_validate_flag, rules_flag, model3D_flag, tensor_flag, exec_file, nanohub_flag, is_movable_flag, ecm_flag, pytest_flag, biwt_flag, parent = None):
         super(PhysiCellXMLCreator, self).__init__(parent)
         if ecm_flag:
             from vis_tab_ecm import Vis 
@@ -106,6 +106,7 @@ def __init__(self, config_file, studio_flag, skip_validate_flag, rules_flag, mod
         self.nanohub_flag = nanohub_flag 
         self.ecm_flag = ecm_flag 
         self.pytest_flag = pytest_flag 
+        self.biwt_flag = biwt_flag
         print("PhysiCellXMLCreator(): self.nanohub_flag= ",self.nanohub_flag)
 
         self.rules_tab_index = None
@@ -340,7 +341,7 @@ def __init__(self, config_file, studio_flag, skip_validate_flag, rules_flag, mod
 
         if self.studio_flag:
             logging.debug(f'studio.py: creating ICs, Run, and Plot tabs')
-            self.ics_tab = ICs(self.config_tab, self.celldef_tab, False, False, False)
+            self.ics_tab = ICs(self.config_tab, self.celldef_tab, self.biwt_flag)
             self.ics_tab.fill_celltype_combobox()
             self.ics_tab.reset_info()
 
@@ -1317,6 +1318,7 @@ def main():
     nanohub_flag = False
     is_movable_flag = False
     pytest_flag = False
+    biwt_flag = False
     try:
         parser = argparse.ArgumentParser(description='PhysiCell Studio.')
 
@@ -1329,6 +1331,7 @@ def main():
         # parser.add_argument("--is_movable", help="checkbox for mechanics is_movable", action="store_true")
         parser.add_argument("-c", "--config", type=str, help="config file (.xml)")
         parser.add_argument("-e", "--exec", type=str, help="executable model")
+        parser.add_argument("--bioinf_import","--biwt", dest="biwt_flag", help="display bioinformatics walkthrough tab on ICs tab", action="store_true")
 
         exec_file = 'project'  # for template sample
 
@@ -1395,6 +1398,8 @@ def main():
             else:
                 print("exec_file is NOT valid: ", args.exec)
                 sys.exit()
+        if args.biwt_flag:
+            biwt_flag = True
     except:
         # print("Error parsing command line args.")
         sys.exit(-1)
@@ -1468,7 +1473,7 @@ def main():
             # print("Warning: Rules module not found.\n")
 
     # print("calling PhysiCellXMLCreator with rules_flag= ",rules_flag)
-    ex = PhysiCellXMLCreator(config_file, studio_flag, skip_validate_flag, rules_flag, model3D_flag, tensor_flag, exec_file, nanohub_flag, is_movable_flag, ecm_flag, pytest_flag)
+    ex = PhysiCellXMLCreator(config_file, studio_flag, skip_validate_flag, rules_flag, model3D_flag, tensor_flag, exec_file, nanohub_flag, is_movable_flag, ecm_flag, pytest_flag, biwt_flag)
     print("size=",ex.size())  # = PyQt5.QtCore.QSize(1100, 770)
     # ex.setFixedWidth(1101)  # = PyQt5.QtCore.QSize(1100, 770)
     # print("width=",ex.size())