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‎analysis/plot_data_ellip.py‎

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"""
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Provide simple plotting functionality for PhysiCell output results.
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Authors:
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Randy Heiland (heiland@iu.edu)
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Dr. Paul Macklin (macklinp@iu.edu)
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--- Versions ---
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0.1 - initial version
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"""
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# https://doc.qt.io/qtforpython/gettingstarted.html
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import os
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import sys
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import getopt
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import shutil
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from pathlib import Path
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import xml.etree.ElementTree as ET # https://docs.python.org/2/library/xml.etree.elementtree.html
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from xml.dom import minidom
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from PyQt5 import QtCore, QtGui
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from PyQt5.QtWidgets import *
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from vis_tab_ellipse import Vis
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def SingleBrowse(self):
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# if len(self.csv) < 2:
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filePath = QFileDialog.getOpenFileName(self,'',".",'*.xml')
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# if filePath != "" and not filePath in self.csv:
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# self.csv.append(filePath)
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# print(self.csv)
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class PhysiCellXMLCreator(QWidget):
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# def __init__(self, parent = None):
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def __init__(self, parent = None):
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super(PhysiCellXMLCreator, self).__init__(parent)
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self.title_prefix = "PhysiCell Visualization"
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self.setWindowTitle(self.title_prefix)
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# Menus
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vlayout = QVBoxLayout(self)
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# vlayout.setContentsMargins(5, 35, 5, 5)
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# menuWidget = QWidget(self.menu())
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# vlayout.addWidget(menuWidget)
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# self.setWindowIcon(self.style().standardIcon(getattr(QStyle, 'SP_DialogNoButton')))
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# self.setWindowIcon(QtGui.QIcon('physicell_logo_25pct.png'))
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# self.grid = QGridLayout()
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# lay.addLayout(self.grid)
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self.setLayout(vlayout)
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# self.setMinimumSize(400, 790) # width, height (height >= Cell Types|Death params)
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# self.setMinimumSize(400, 500) # width, height (height >= Cell Types|Death params)
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# self.setMinimumSize(800, 620) # width, height (height >= Cell Types|Death params)
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# self.setMinimumSize(800, 660) # width, height (height >= Cell Types|Death params)
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# self.setMinimumSize(800, 800) # width, height (height >= Cell Types|Death params)
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# self.setMinimumSize(700, 770) # width, height (height >= Cell Types|Death params)
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self.setMinimumSize(800, 770) # width, height (height >= Cell Types|Death params)
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# self.setMinimumSize(600, 600) # width, height (height >= Cell Types|Death params)
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# self.resize(400, 790) # width, height (height >= Cell Types|Death params)
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# self.menubar = QtWidgets.QMenuBar(self)
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# self.file_menu = QtWidgets.QMenu('File')
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# self.file_menu.insertAction("Open")
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# self.menubar.addMenu(self.file_menu)
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# GUI tabs
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# By default, let's startup the app with a default of template2D (a copy)
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# self.new_model_cb() # default on startup
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# read_file = "../data/subcellular_flat.xml"
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# read_file = "../data/cancer_biorobots_flat.xml"
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# read_file = "../data/pred_prey_flat.xml"
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model_name = "pred_prey_flat"
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model_name = "biorobots_flat"
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model_name = "cancer_biorobots_flat"
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model_name = "test1"
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model_name = "test-gui"
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model_name = "covid19_v5_flat"
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model_name = "template"
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# model_name = "randy_test" #rwh
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# read_file = "data/" + model_name + ".xml"
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# then what??
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# binDirectory = os.path.realpath(os.path.abspath(__file__))
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binDirectory = os.path.dirname(os.path.abspath(__file__))
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dataDirectory = os.path.join(binDirectory,'..','data')
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# self.tree = ET.parse(self.config_file)
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# self.xml_root = self.tree.getroot()
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#------------------
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tabWidget = QTabWidget()
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self.vis_tab = Vis()
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# self.vis_tab.xml_root = self.xml_root
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tabWidget.addTab(self.vis_tab,"")
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vlayout.addWidget(tabWidget)
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# self.addTab(self.sbml_tab,"SBML")
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tabWidget.setCurrentIndex(0) # Config (default)
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def menu(self):
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menubar = QMenuBar(self)
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menubar.setNativeMenuBar(False)
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#--------------
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file_menu = menubar.addMenu('&File')
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# # file_menu.addAction("Open", self.open_as_cb, QtGui.QKeySequence('Ctrl+o'))
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# file_menu.addAction("Save", self.save_cb, QtGui.QKeySequence('Ctrl+s'))
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menubar.adjustSize() # Argh. Otherwise, only 1st menu appears, with ">>" to others!
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def main():
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inputfile = ''
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app = QApplication(sys.argv)
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ex = PhysiCellXMLCreator()
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# ex.setGeometry(100,100, 800,600)
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ex.show()
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sys.exit(app.exec_())
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if __name__ == '__main__':
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main()

‎analysis/plot_ellip.py‎

Lines changed: 128 additions & 0 deletions
Original file line numberDiff line numberDiff line change
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"""
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Provide simple plotting functionality for PhysiCell output results.
3+
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Authors:
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Randy Heiland (heiland@iu.edu)
6+
Dr. Paul Macklin (macklinp@iu.edu)
7+
8+
--- Versions ---
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0.1 - initial version
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"""
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# https://doc.qt.io/qtforpython/gettingstarted.html
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import os
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import sys
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import getopt
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import shutil
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from pathlib import Path
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import xml.etree.ElementTree as ET # https://docs.python.org/2/library/xml.etree.elementtree.html
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from xml.dom import minidom
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from PyQt5 import QtCore, QtGui
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from PyQt5.QtWidgets import *
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from vis_tab_cells_ellipse import Vis
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def SingleBrowse(self):
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# if len(self.csv) < 2:
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filePath = QFileDialog.getOpenFileName(self,'',".",'*.xml')
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# if filePath != "" and not filePath in self.csv:
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# self.csv.append(filePath)
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# print(self.csv)
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class PhysiCellXMLCreator(QWidget):
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# def __init__(self, parent = None):
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def __init__(self, parent = None):
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super(PhysiCellXMLCreator, self).__init__(parent)
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self.title_prefix = "PhysiCell Visualization"
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self.setWindowTitle(self.title_prefix)
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# Menus
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vlayout = QVBoxLayout(self)
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# vlayout.setContentsMargins(5, 35, 5, 5)
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# menuWidget = QWidget(self.menu())
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# vlayout.addWidget(menuWidget)
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# self.setWindowIcon(self.style().standardIcon(getattr(QStyle, 'SP_DialogNoButton')))
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# self.setWindowIcon(QtGui.QIcon('physicell_logo_25pct.png'))
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# self.grid = QGridLayout()
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# lay.addLayout(self.grid)
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self.setLayout(vlayout)
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# self.setMinimumSize(400, 790) # width, height (height >= Cell Types|Death params)
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# self.setMinimumSize(400, 500) # width, height (height >= Cell Types|Death params)
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# self.setMinimumSize(800, 620) # width, height (height >= Cell Types|Death params)
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# self.setMinimumSize(800, 660) # width, height (height >= Cell Types|Death params)
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# self.setMinimumSize(800, 800) # width, height (height >= Cell Types|Death params)
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self.setMinimumSize(700, 770) # width, height (height >= Cell Types|Death params)
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# self.setMinimumSize(600, 600) # width, height (height >= Cell Types|Death params)
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# self.resize(400, 790) # width, height (height >= Cell Types|Death params)
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# self.menubar = QtWidgets.QMenuBar(self)
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# self.file_menu = QtWidgets.QMenu('File')
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# self.file_menu.insertAction("Open")
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# self.menubar.addMenu(self.file_menu)
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# GUI tabs
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# By default, let's startup the app with a default of template2D (a copy)
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# self.new_model_cb() # default on startup
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# read_file = "../data/subcellular_flat.xml"
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# read_file = "../data/cancer_biorobots_flat.xml"
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# read_file = "../data/pred_prey_flat.xml"
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model_name = "pred_prey_flat"
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model_name = "biorobots_flat"
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model_name = "cancer_biorobots_flat"
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model_name = "test1"
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model_name = "test-gui"
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model_name = "covid19_v5_flat"
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model_name = "template"
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# model_name = "randy_test" #rwh
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# read_file = "data/" + model_name + ".xml"
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# then what??
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# binDirectory = os.path.realpath(os.path.abspath(__file__))
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binDirectory = os.path.dirname(os.path.abspath(__file__))
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dataDirectory = os.path.join(binDirectory,'..','data')
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# self.tree = ET.parse(self.config_file)
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# self.xml_root = self.tree.getroot()
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#------------------
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tabWidget = QTabWidget()
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self.vis_tab = Vis()
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# self.vis_tab.xml_root = self.xml_root
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tabWidget.addTab(self.vis_tab,"Plot")
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vlayout.addWidget(tabWidget)
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# self.addTab(self.sbml_tab,"SBML")
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tabWidget.setCurrentIndex(0) # Config (default)
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def menu(self):
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menubar = QMenuBar(self)
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menubar.setNativeMenuBar(False)
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#--------------
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file_menu = menubar.addMenu('&File')
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# # file_menu.addAction("Open", self.open_as_cb, QtGui.QKeySequence('Ctrl+o'))
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# file_menu.addAction("Save", self.save_cb, QtGui.QKeySequence('Ctrl+s'))
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menubar.adjustSize() # Argh. Otherwise, only 1st menu appears, with ">>" to others!
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def main():
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inputfile = ''
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app = QApplication(sys.argv)
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ex = PhysiCellXMLCreator()
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# ex.setGeometry(100,100, 800,600)
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ex.show()
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sys.exit(app.exec_())
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if __name__ == '__main__':
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main()

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