"""
Description:
This script was written to create and display figures comparing locations of two different patients. This is used to
check the analysis points quickly to make sure they make sense and also to confirm that we are seeing similar
landmarks in the ultrasound images across patients.
Getting started:
A dialog box will appear, type in the desired location (for example UA_L for upper arm lateral images). A
checkbox list will appear with all of the available locations and patients that were analyzed using TA_sfm
software. Select the six trials you would like to include. At this point, the code can only produce images for
anatomical trials (proximal, central, and distal) for each limb anatomical location.
Original Author:
Erica Morrill
Department of Biomedical Engineering
Lerner Research Institute
Cleveland Clinic
Cleveland, OH
morrile2@ccf.org
"""
import xml.etree.ElementTree as ET
import os
import Tkinter as tk
import pandas
import tkFileDialog
import matplotlib.pyplot as plt
from matplotlib.ticker import MaxNLocator
import numpy as np
import tkSimpleDialog
from scipy.misc import imread, imshow
class FileSelectionApp(tk.Tk):
"""Application to display all of the trials in a list"""
def __init__(self):
tk.Tk.__init__(self)
home = os.path.expanduser('~')
for dirname, subdirList, fileList in os.walk(home):
for dir in subdirList:
if "MULTIS_test" in dir and "studies" not in dirname:
multis_dir = dirname + '/' + dir
print multis_dir
try:
multis_dir
except NameError:
multis_dir = tkFileDialog.askdirectory(title="Open MULTIS trials directory")
self.directory = multis_dir
self.getSubjects()
self.title('Select Files')
self.columnconfigure(0, weight=1)
self.var = []
self.i = 0
for item in self.subFiles:
self.var.append(tk.IntVar())
c = tk.Checkbutton(self, text=item, variable=self.var[self.i])
c.grid(column = 0, row=self.i, sticky='w')
self.i +=1
# self.minsize(200, 100/(self.i))
tk.Button(self, text="Okay", command=self.checkBoxes).grid(row=2, column =1, sticky='ens')
tk.Button(self, text="Select All", command=self.SelectAll).grid(row=0, column=1, sticky='ens')
tk.Button(self, text="Clear Selection", command=self.ClearSelection).grid(row=1, column=1, sticky = 'ens')
def yview(self, *args):
apply(self.yview, args)
def checkBoxes(self):
locations = ['LA_A', 'LA_L', 'LA_P', 'LA_M', 'UA_A', 'UA_L', 'UA_P', 'UA_M', 'LL_A', 'LL_L', 'LL_P', 'LL_M',
'UL_A', 'UL_L', 'UL_P', 'UL_M']
# locations = ['LA_A'] #Used for testing
for l1 in locations:
for l2 in ['C', 'C', 'D']:
loc = l1 + l2
count = 0
self.text = loc
self.images = []
self.num = []
for bb in self.var:
if bb.get() == 1:
# print(self.subFiles)
files, nums = self.getImages(loc, self.dir[count])
self.images = self.images + files
self.num = self.num + nums
count += 1
zipped = zip(self.images, self.num)
zipped.sort(key=lambda t:t[1])
self.images, self.num = zip(*zipped)
# self.destroy()
self.plot_data()
self.quit()
def plot_data(self):
fig_idx = len(self.images)/25+1
for i in range(fig_idx):
images = self.images[i*25:(i+1)*25]
num = self.num[i*25:(i+1)*25]
fig, ax = plt.subplots(5, 5, figsize = (16,13))
if self.text[0] == 'U':
title = 'Upper'
elif self.text[0] == 'L':
title = 'Lower'
if self.text[1] == 'A':
title += ' Arm'
elif self.text[1] == 'L':
title += ' Leg'
if self.text[3] == 'A':
title += ' Anterior'
elif self.text[3] == 'L':
title += ' Lateral'
elif self.text[3] == 'P':
title += ' Posterior'
elif self.text[3] == 'M':
title += ' Medial'
if self.text[4] == 'P':
title += ' Proximal'
elif self.text[4] == 'C':
title += ' Central'
elif self.text[4] == 'D':
title += ' Distal'
for p, img in enumerate(images):
ax[p//5,p%5].imshow(imread(img))
ax[p // 5, p % 5].set_xlim([165, 1170])
ax[p // 5, p % 5].set_ylim([875, 125])
ax[p // 5, p % 5].axis("off")
ax[p//5,p%5].set_title("MULTIS"+num[p])
for p in range(len(images), 25):
ax[p//5, p%5].axis("off")
fig.suptitle(title, fontsize=20, x = 0.525)
fig.tight_layout()
fig.subplots_adjust(top = 0.92, left = 0.05, right = 0.95)
if not os.path.isdir(self.directory+'/SummaryFigures/'):
os.makedirs(self.directory+'/SummaryFigures/')
plt.savefig(self.directory + '/SummaryFigures/' + self.text+'_' + str(i) +'.png')
fig.close()
# plt.show()
def SelectAll(self):
for bb in self.var:
bb.set(1)
def ClearSelection(self):
for bb in self.var:
bb.set(0)
def getSubjects(self):
self.subFiles = []
self.dir = []
for dirname,subdirList,fileList in os.walk(self.directory):
for file in fileList:
if "TA_inclusion.xml" in file:
self.dir.append(os.path.split(os.path.split(dirname)[0])[0])
self.subFiles.append(os.path.split(os.path.split(os.path.split(dirname)[0])[0])[1])
sortedTrials = sorted(zip(self.subFiles, self.dir))
self.subFiles, self.dir = zip(*sortedTrials)
def getImages(self, location, directory):
loc_files = []
nums = []
thick_xml_list = self.parseXMLinclusion(location, os.path.join(os.path.join(os.path.join(directory,'TissueThickness'), 'UltrasoundManual'), os.path.split(directory)[1]+"_TA_inclusion.xml"))
# print thick_xml_list
for th_xml in thick_xml_list:
loc_files.append(os.path.join(os.path.join(os.path.join(directory, os.path.split(th_xml)[0]), 'ThicknessPNG'), os.path.split(th_xml)[1][0:-4]+'.png'))
nums.append(os.path.split(th_xml)[1][10:13])
# print loc_files, nums
return loc_files, nums
def parseXMLinclusion(self, location, inclusion):
doc = ET.parse(inclusion)
root = doc.getroot()
thickness_xmls = []
for child in root:
for subChild in child:
XML = subChild.attrib["Anatomical"]
if XML != "None" and XML[-28:-27] == "A" and XML[-34:-29] == location:
thickness_xmls.append(XML)
return thickness_xmls
if __name__ == "__main__":
app = FileSelectionApp()
app.mainloop()