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Merge pull request #99 from PhysiCell-Tools/development
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@rheiland
rheiland authored Jun 16, 2023
2 parents b2a4872 + d5b64ab commit 0de1bf8
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Showing 4 changed files with 163 additions and 55 deletions.
2 changes: 1 addition & 1 deletion VERSION.txt
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@@ -1 +1 @@
2.26.2
2.26.3
190 changes: 147 additions & 43 deletions bin/studio.py
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Expand Up @@ -20,6 +20,7 @@
import logging
import traceback
import shutil # for possible copy of file
import glob
from pathlib import Path
import xml.etree.ElementTree as ET # https://docs.python.org/2/library/xml.etree.elementtree.html
# from xml.dom import minidom # possibly explore later if we want to access/update *everything* in the DOM
Expand Down Expand Up @@ -598,63 +599,77 @@ def menu(self):

#------
file_menu.addSeparator()
samples_menu = file_menu.addMenu("Samples")
file_menu.addAction("Save user project", self.save_user_proj_cb)
file_menu.addAction("Load user project", self.load_user_proj_cb)
# user_proj_menu = file_menu.addMenu("User project")

template_act = QAction('template', self)
samples_menu.addAction(template_act)
template_act.triggered.connect(self.template_cb)
# save_user_proj = QAction('Save', self)
# user_proj_menu.addAction(save_user_proj)
# save_user_proj.triggered.connect(self.save_user_proj_cb)

biorobots_act = QAction('biorobots', self)
samples_menu.addAction(biorobots_act)
biorobots_act.triggered.connect(self.biorobots_cb)
# load_user_proj = QAction('Load', self)
# user_proj_menu.addAction(load_user_proj)
# load_user_proj.triggered.connect(self.load_user_proj_cb)

cancer_biorobots_act = QAction('cancer biorobots', self)
samples_menu.addAction(cancer_biorobots_act)
cancer_biorobots_act.triggered.connect(self.cancer_biorobots_cb)
#------
# file_menu.addSeparator()
# samples_menu = file_menu.addMenu("Samples")

# template_act = QAction('template', self)
# samples_menu.addAction(template_act)
# template_act.triggered.connect(self.template_cb)

# biorobots_act = QAction('biorobots', self)
# samples_menu.addAction(biorobots_act)
# biorobots_act.triggered.connect(self.biorobots_cb)

# cancer_biorobots_act = QAction('cancer biorobots', self)
# samples_menu.addAction(cancer_biorobots_act)
# cancer_biorobots_act.triggered.connect(self.cancer_biorobots_cb)

hetero_act = QAction('heterogeneity', self)
samples_menu.addAction(hetero_act)
hetero_act.triggered.connect(self.hetero_cb)
# hetero_act = QAction('heterogeneity', self)
# samples_menu.addAction(hetero_act)
# hetero_act.triggered.connect(self.hetero_cb)

pred_prey_act = QAction('predator-prey-farmer', self)
samples_menu.addAction(pred_prey_act)
pred_prey_act.triggered.connect(self.pred_prey_cb)
# pred_prey_act = QAction('predator-prey-farmer', self)
# samples_menu.addAction(pred_prey_act)
# pred_prey_act.triggered.connect(self.pred_prey_cb)

virus_mac_act = QAction('virus-macrophage', self)
samples_menu.addAction(virus_mac_act)
virus_mac_act.triggered.connect(self.virus_mac_cb)
# virus_mac_act = QAction('virus-macrophage', self)
# samples_menu.addAction(virus_mac_act)
# virus_mac_act.triggered.connect(self.virus_mac_cb)

worm_act = QAction('worm', self)
samples_menu.addAction(worm_act)
worm_act.triggered.connect(self.worm_cb)
# worm_act = QAction('worm', self)
# samples_menu.addAction(worm_act)
# worm_act.triggered.connect(self.worm_cb)

interactions_act = QAction('interactions', self)
samples_menu.addAction(interactions_act)
interactions_act.triggered.connect(self.interactions_cb)
# interactions_act = QAction('interactions', self)
# samples_menu.addAction(interactions_act)
# interactions_act.triggered.connect(self.interactions_cb)

mechano_act = QAction('mechano', self)
samples_menu.addAction(mechano_act)
mechano_act.triggered.connect(self.mechano_cb)
# mechano_act = QAction('mechano', self)
# samples_menu.addAction(mechano_act)
# mechano_act.triggered.connect(self.mechano_cb)

cancer_immune_act = QAction('cancer immune (3D)', self)
samples_menu.addAction(cancer_immune_act)
cancer_immune_act.triggered.connect(self.cancer_immune_cb)
# cancer_immune_act = QAction('cancer immune (3D)', self)
# samples_menu.addAction(cancer_immune_act)
# cancer_immune_act.triggered.connect(self.cancer_immune_cb)

physiboss_cell_lines_act = QAction('PhysiBoSS cell lines', self)
samples_menu.addAction(physiboss_cell_lines_act)
physiboss_cell_lines_act.triggered.connect(self.physiboss_cell_lines_cb)
# physiboss_cell_lines_act = QAction('PhysiBoSS cell lines', self)
# samples_menu.addAction(physiboss_cell_lines_act)
# physiboss_cell_lines_act.triggered.connect(self.physiboss_cell_lines_cb)

subcell_act = QAction('subcellular', self)
# samples_menu.addAction(subcell_act)
subcell_act.triggered.connect(self.subcell_cb)
# subcell_act = QAction('subcellular', self)
# # samples_menu.addAction(subcell_act)
# subcell_act.triggered.connect(self.subcell_cb)

covid19_act = QAction('covid19_v5', self)
# samples_menu.addAction(covid19_act)
covid19_act.triggered.connect(self.covid19_cb)
# covid19_act = QAction('covid19_v5', self)
# # samples_menu.addAction(covid19_act)
# covid19_act.triggered.connect(self.covid19_cb)

test_gui_act = QAction('test-gui', self)
# samples_menu.addAction(test_gui_act)
test_gui_act.triggered.connect(self.test_gui_cb)
# test_gui_act = QAction('test-gui', self)
# # samples_menu.addAction(test_gui_act)
# test_gui_act.triggered.connect(self.test_gui_cb)

# else:
# file_menu.addAction("Save as mymodel.xml", self.save_as_cb)
Expand Down Expand Up @@ -812,6 +827,7 @@ def indent(elem, level=0):
elem.tail = i


#---------------------------------
def save_as_cb(self):
# print("------ save_as_cb():")
self.celldef_tab.check_valid_cell_defs()
Expand Down Expand Up @@ -893,7 +909,95 @@ def save_cb(self):
except CellDefException as e:
self.show_error_message(str(e) + " : save_cb(): Error: Please finish the definition before saving.")

#---------------------------------
def save_user_proj_cb(self):
# print("------ save_user_proj_cb():")
# self.celldef_tab.check_valid_cell_defs()

dialog = QFileDialog(self)
dialog.setFileMode(QFileDialog.Directory)
folder_path = dialog.getExistingDirectory(None, "Select project folder","user_projects",QFileDialog.ShowDirsOnly)
print("save_user_proj_cb(): folder_path=",folder_path)
# e.g., /Users/heiland/dev/PhysiCell_v1.12.0/user_projects/rwh3

# mkdir -p ./user_projects
# mkdir -p ./user_projects/rwh1
# mkdir -p ./user_projects/rwh1/custom_modules
# mkdir -p ./user_projects/rwh1/config
# cp main.cpp ./user_projects/rwh1
# cp Makefile ./user_projects/rwh1
# cp VERSION.txt ./user_projects/rwh1
# cp ./config/* ./user_projects/rwh1/config
# cp ./custom_modules/* ./user_projects/rwh1/custom_modules

for f in ["main.cpp", "Makefile", "VERSION.txt"]:
try:
shutil.copy(f, folder_path)
except:
print(f"--- Warning: cannot save {f}")

#---------
subdir = Path(folder_path, "config")
try:
os.makedirs(subdir)
except:
print(f"--- Warning: {subdir} already exists.")

try:
for f in glob.glob("config/*"):
shutil.copy(f, subdir)
except:
print(f"--- Warning: cannot copy config/*")

#---------
subdir = Path(folder_path, "custom_modules")
try:
os.makedirs(subdir)
except:
print(f"--- Warning: {dir1} already exists.")

try:
for f in glob.glob("custom_modules/*"):
shutil.copy(f, subdir)
except:
print(f"--- Warning: cannot copy custom_modules/*")

#---------------------------------
def load_user_proj_cb(self):
try:
dialog = QFileDialog(self)
dialog.setFileMode(QFileDialog.Directory)
folder_path = dialog.getExistingDirectory(None, "Select project folder","user_projects",QFileDialog.ShowDirsOnly)
print("load_user_proj_cb(): folder_path=",folder_path)

# cp ./user_projects/rwh1/main.cpp .
# cp ./user_projects/rwh1/Makefile .
# cp ./user_projects/rwh1/config/* ./config/
# cp ./user_projects/rwh1/custom_modules/* ./custom_modules/

for f in ["main.cpp", "Makefile"]:
try:
f2 = os.path.join(folder_path, f)
shutil.copy(f2, '.')
print(f"copy {f2} to root")
except:
print(f"--- Warning: cannot copy {f2}")

for d in ["config", "custom_modules"]:
d1 = os.path.join(folder_path, d)
print(f"d1 = {d1}")
for f in glob.glob(str(d1) + "/*"):
print(f"try copying {f} to {d}")
shutil.copy(f, d)

except:
msgBox = QMessageBox()
msgBox.setIcon(QMessageBox.Information)
msgBox.setText("load_user_proj_cb(): Possible failure. See terminal output.")
msgBox.setStandardButtons(QMessageBox.Ok | QMessageBox.Cancel)
returnValue = msgBox.exec()

#---------------------------------
def validate_cb(self): # not used currently
msgBox = QMessageBox()
msgBox.setIcon(QMessageBox.Information)
Expand Down
26 changes: 15 additions & 11 deletions bin/vis_base.py
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Expand Up @@ -2171,17 +2171,21 @@ def fix_cmap_toggle_cb(self,bval):
# print("field_name= ",field_name)
# print(self.cmap_fixed_toggle.value)
# if (self.colormap_fixed_toggle.value): # toggle on fixed range
if (bval): # toggle on fixed range
# self.colormap_min.disabled = False
# self.colormap_max.disabled = False
self.field_min_max[field_name][0] = self.cmin.text
self.field_min_max[field_name][1] = self.cmax.text
self.field_min_max[field_name][2] = True
# self.save_min_max.disabled = False
else: # toggle off fixed range
# self.colormap_min.disabled = True
# self.colormap_max.disabled = True
self.field_min_max[field_name][2] = False
# --- rwh: TODO
try:
if (bval): # toggle on fixed range
# self.colormap_min.disabled = False
# self.colormap_max.disabled = False
self.field_min_max[field_name][0] = self.cmin.text
self.field_min_max[field_name][1] = self.cmax.text
self.field_min_max[field_name][2] = True
# self.save_min_max.disabled = False
else: # toggle off fixed range
# self.colormap_min.disabled = True
# self.colormap_max.disabled = True
self.field_min_max[field_name][2] = False
except:
print("------- vis_base: fix_cmap_toggle_cb(): exception updating field_min_max for ",field_name)

# print("\n>>> calling update_plots() from "+ inspect.stack()[0][3])
self.update_plots()
Expand Down
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