def Extract_frame():
print("Choose video file....")
fname = askopenfilename(initialdir = '/home/andyc/Videos/')
print("where do you want to save?(choose folder)\n")
savepath = askdirectory(initialdir = '/home/andyc/image/')
while savepath == '':
print("wrong folder!!\n")
print("where do you want to save?(choose folder)\n")
savepath = askdirectory(initialdir = '/home/andyc/image/')
savepath = savepath+'/'
video = cv2.VideoCapture(fname)
if video.isOpened():
rval,frame = video.read()
else:
rval = False
idx = 0
while rval:
print("Extracting {0} frame".format(idx))
rval,frame = video.read()
name = savepath+str(idx).zfill(6)+'.jpg'
if rval:
cv2.imwrite(name,frame)
idx = idx+1
video.release()
return savepath
def main():
root=Tk()
root.withdraw() #Get rid of visible default TK base window
newPath = tkFileDialog.askdirectory(initialdir='/', title='Select NEW VSDX Documents Folder')
oldPath = tkFileDialog.askdirectory(initialdir='/', title='Select OLD VSDX Documents Folder')
destPath = tkFileDialog.askdirectory(initialdir='/', title='Select Comparison Results Folder')
oldFiles = getOldFiles(oldPath)
newFiles = getNewFiles(newPath)
# Open report.txt file
rptFilename = destPath + '/' + 'ComparisonReport_' + str(date.today()) + '.txt'
with open(rptFilename, 'w') as rptFile:
rptFile.write('Comparison Report for %s\n\n' % str(date.today()))
rptFile.write('Total OLD Files: %d\n' % len(oldFiles))
rptFile.write('Total NEW Files: %d\n\n' % len(newFiles))
# Compare the files
for newFile in newFiles:
if newFile in oldFiles:
compareFiles(oldPath, newPath, destPath, newFile)
else:
rptFile.write('New file added: %s\n' % newFile)
rptFile.write('\n\n')
for oldFile in oldFiles:
if oldFile not in newFiles:
rptFile.write('Old file dropped: %s\n' % oldFile)
def getPath():
root = Tk()
root.withdraw()
InputPath = askdirectory(title="Choose Converting Picture Input Path")
OutputPath = askdirectory(title="Choose Converting Picture Output Path")
root.destroy()
return InputPath, OutputPath
def getMayaDir(self):
if self.plateform == "darwin":
dir=self.sharedDirectory+"/Autodesk/maya/2011/plug-ins/"
if not os.path.exists(dir):
x = askdirectory(initialdir=self.progDirectory, title="where is MAYA2011 plugin directory")
dir = x
self.dir[3].set(dir)
self.softdir[3] = dir
elif self.plateform == "win32":
dir=self.findDirectoryFrom("Maya2011",self.progDirectory+os.sep+"Autodesk"+os.sep)
if len(dir) ==0 :
x = askdirectory(initialdir=self.progDirectory, title="where is MAYA2011 bin/plugins directory")
dir = x
self.dir[3].set(dir)
self.softdir[3] = dir
elif len(dir) == 1 :
dir = dir[0]
dir = dir +os.sep+"bin"+os.sep+"plug-ins"
self.dir[3].set(dir)
self.softdir[3] = dir
else :
self.chooseDirectory(3,dir)
elif self.automaticSearch and dir is None:
dir=self.findDirectory("maya2011",self.rootDirectory)
dir = dir.replace(" ","\ ")
self.dir[3].set(dir)
self.softdir[3] = dir
def askdirectory(self):
"""Returns a selected directoryname."""
print(tkFileDialog.askdirectory(**self.dir_opt))
return tkFileDialog.askdirectory(**self.dir_opt)
def getPaths():
global pathFirst
global pathSecond
root = tk.Tk()
root.withdraw()
pathFirst = tkfd.askdirectory(title="Select First Folder Path")
pathSecond = tkfd.askdirectory(title="Select Second Folder Path")
def askdirectory(self,button_name):
#gets the directory name
if button_name=='proj':
self.dirname_data.set(tkFileDialog.askdirectory())
elif button_name=='beam':
self.dirname_lf.set(tkFileDialog.askdirectory())
elif button_name=='dark':
self.dirname_dc.set(tkFileDialog.askdirectory())
def gettemplate(self):
if os.path.exists(self.templatepath):
l = tkFileDialog.askdirectory(initialdir=self.templatepath, mustexist=True)
else:
l = tkFileDialog.askdirectory(mustexist=True)
if os.path.exists(l):
self.templatepath = l
self.entryboxes['Template'].delete(0,END)
self.entryboxes['Template'].insert(0, self.templatepath)
def getlocation(self):
if os.path.exists(self.location):
l = tkFileDialog.askdirectory(initialdir=self.location, mustexist=True)
else:
l = tkFileDialog.askdirectory(mustexist=True)
if os.path.exists(l):
self.location = l
self.entryboxes['Location'].delete(0,END)
self.entryboxes['Location'].insert(0, self.location)
def _ask_path_to_directory(self):
""" Ask a path to the destination directory. If a dir has been already specified,
open the choice window showing this dir. """
if not self.homeDir:
path = askdirectory(**_DialogueLabels.save_output_directory_choice)
else:
path = askdirectory(initialdir = self.homeDir, **_DialogueLabels.save_output_directory_choice)
if path:
self.homeDir = path
return path
def getDir(initialDir=""):
root = tk.Tk()
root.withdraw()
if(initialDir != ""):
file_path = tkFileDialog.askdirectory(initialdir=initialDir)
else:
file_path = tkFileDialog.askdirectory()
root.destroy()
return file_path
def extracter(spreadsheet, column_name):
"""
The extracter moves files.
Arguments input_folder and output_folder are set through GUI.
Based on the values in the column called column_name in the spreadsheet, files are copied from input_folder to output_folder.
Here, these are the gilbert_numbers in the spreadsheet fed from main().
The are matched to the file names.
Each gilber_number gets its own directory in the output_folder.
output_folder should be empty, at least not contain the same gilbert_numbers already.
Also copies all speaker files from input_folder to output_folder.
"""
print header, "Running the extracter."
root=Tkinter.Tk()
root.withdraw()
root.update()
input_folder=tkFileDialog.askdirectory(title="Inputfolder: Please choose a directory that contains your corpus files")
root=Tkinter.Tk()
root.withdraw()
root.update()
output_folder=tkFileDialog.askdirectory(title="Outputfolder: Please choose a directory to copy files into")
print header, "Copying files from '{}' to '{}'.".format(input_folder, output_folder)
#collecting input files
inputfiles=[]
print "Locating files."
for dirpath, subdirs, files in os.walk(input_folder):
for f in files:
inputfiles.append(os.path.join(dirpath, f))
if len(inputfiles) in [1000,2000,4000,8000,1600,24000]:
print "{} files processed, still working.".format(len(inputfiles))
print "Found {} files.".format(len(inputfiles))
#read from spreadsheet
# with open(spreadsheet, "r") as spreadsheet:
# spreadsheet=pandas.read_csv(spreadsheet, encoding="utf-8")
numbers_to_be_extracted= spreadsheet[column_name].unique()
print header, "Gilbert numbers to be extracted:"
print ",".join([unicode(i) for i in numbers_to_be_extracted])
#copying speaker files
print header, "Copying speaker files."
speakerfiles=[f for f in inputfiles if re.match(".*\.txt", os.path.split(f)[1])]
os.mkdir(os.path.join(output_folder, "speakers"))
for s in speakerfiles:
shutil.copy2(s, os.path.join(output_folder, "speakers"))
#finding relevant input files
result=[]
for number in numbers_to_be_extracted:
print "Processing {}, creating folder '{}'.".format(number, number)
os.mkdir(os.path.join(output_folder, unicode(number)))
regex="(\d+)-(\d+)-(\d+)-"+number.astype('U')+"-(\D+)\.wav"
findings= [f for f in inputfiles if re.match(regex, os.path.split(f)[1])]
result= result+findings
for find in findings:
shutil.copy2(find, os.path.join(output_folder, unicode(number), os.path.split(find)[1]))
print header, "{} files have been copied to {}.".format(len(result), output_folder)
def AskDirectory(self, title='Choose Directory', initialdir="."):
"""Run pop-up menu for user to select directory."""
# This is not an error
# pylint: disable=E1101
if sys.version_info < (3,):
dirname = tkFileDialog.askdirectory(parent=self.master,
initialdir=initialdir,title=title)
else:
dirname = tkFileDialog.askdirectory(parent=self.master,
initialdir=initialdir,title=title)
return dirname # <-- string
def ExpBrowse():
if not self.hasBrowsed:
dir = tkFileDialog.askdirectory(title='Choose a directory',
initialdir=self.initBrowseDir)
self.hasBrowsed = True
else:
dir = tkFileDialog.askdirectory(title='Choose a directory')
if not dir:
return None
#self.addExp_Entry.setvalue(dir)
self.AddExperiment(dir)
def getFolders(self):
self.input_dir = tkFileDialog.askdirectory(
parent=self.parent, title="Please select an input directory for 2dx_automator"
)
if len(self.input_dir) == 0:
raise SystemExit("No input directory selected")
self.output_dir = tkFileDialog.askdirectory(
parent=self.parent, title="Please select an output directory for 2dx_automator"
)
if len(self.output_dir) == 0:
raise SystemExit("No output directory selected")
def getFolders(self):
self.input_dir = tkFileDialog.askdirectory(parent=self.parent, title="Input directory for movies from the DED camera, e.g. /run/user/1001/gvfs/ftp:host=192.168.210.1.port=8021/...")
if len(self.input_dir)==0:
raise SystemExit("No input directory selected")
self.output_dir = tkFileDialog.askdirectory(parent=self.parent, title="Output directory for averages and other files, e.g. /mnt/cina-qnap01/.../DC_averages")
if len(self.output_dir)==0:
raise SystemExit("No averages output directory selected")
stack_dir = tkFileDialog.askdirectory(parent=self.parent, title="Output directory for aligned stacks, e.g. /mnt/cina-qnap01/.../DC_stacks")
if len(stack_dir)==0:
raise SystemExit("No stack-output directory selected")
self.export_location_stack = stack_dir
def pathOpen(option=0):
if option is 0:
userpath.set(tkFileDialog.askdirectory(parent=root))
cfg.userPath = userpath.get()
elif option is 1:
gtpath.set(tkFileDialog.askdirectory(parent=root))
if os.path.isfile(os.path.join(gtpath.get(), "data.mat")):
cfg.gtPath = gtpath.get()
cfg.loadGT()
tempo.set(cfg.tempo)
duration.set(cfg.duration)
else:
tkMessageBox.showinfo("ERROR", "Missing data file. Please choose a different folder.")
def askInstallPrefix(self):
"""
command for search button
"""
initDir=self.installP.get()
newPrefix=""
if os.path.exists(initDir):
newPrefix=tkFileDialog.askdirectory(parent=self,initialdir=initDir,mustexist=1)
else:
newPrefix=tkFileDialog.askdirectory(parent=self,mustexist=1)
if newPrefix:
self.installP.delete(0, Tkinter.END)
self.installP.insert(0, newPrefix)
def __init__(self):
"""Constructor"""
self.workspace = arcpy.env.workspace = tkFileDialog.askdirectory(initialdir = INITDIR, parent=tkRoot, title = 'Choose workspace (ArcPy)', mustexist = True)
arcpy.env.scratchWorkspace = tkFileDialog.askdirectory(initialdir = INITDIR+"\scratchworkspace", parent=tkRoot, title = 'Choose scratch workspace (ArcPy)', mustexist = True)
#Arcpy specific
arcpy.CheckOutExtension("spatial") #Load sa license
arcpy.env.overwriteOutput = True #Enable overwrite existing data
arcpy.env.outputCoordinateSystem = OUTPUT_COORDINATESYSTEM #"Coordinate Systems/Projected Coordinate Systems/UTM/WGS 1984/Northern Hemisphere/WGS 1984 UTM Zone 43N.prj"
self.pArcPyTools = ArcPyTools() #Init of own tool class
def file_select(self, file_type):
#file_type is internal, uses string ints (goes in order of layout in __init__
if file_type == '0':
#this is bwa_directory
self.bwa_directory_path.config(state = NORMAL)
self.bwa_directory_path.delete(1.0, END)
file_name = tkfd.askdirectory(parent=self, title='Select BWA Aligner directory')
self.bwa_directory_path.insert(INSERT, file_name)
self.bwa_directory_path.config(state = DISABLED)
with open('paths.txt', 'r') as file:
lines = file.readlines()
lines[0] = file_name + '\n'
with open('paths.txt', 'w') as file:
file.writelines(lines)
elif file_type=='1':
#this is picard_directory
self.picard_directory_path.config(state = NORMAL)
self.picard_directory_path.delete(1.0, END)
file_name = tkfd.askdirectory(parent=self, title='Select Picard Tools directory')
self.picard_directory_path.insert(INSERT, file_name)
self.picard_directory_path.config(state = DISABLED)
with open('paths.txt', 'r') as file:
lines = file.readlines()
lines[1] = file_name + '\n'
with open('paths.txt', 'w') as file:
file.writelines(lines)
elif file_type=='2':
#this is samtools_directory
self.samtools_directory_path.config(state = NORMAL)
self.samtools_directory_path.delete(1.0, END)
file_name = tkfd.askdirectory(parent=self, title='Select SamTools directory')
self.samtools_directory_path.insert(INSERT, file_name)
self.samtools_directory_path.config(state = DISABLED)
with open('paths.txt', 'r') as file:
lines = file.readlines()
lines[2] = file_name + '\n'
with open('paths.txt', 'w') as file:
file.writelines(lines)
else:
#this is the output directoyr
self.out_dir_path.config(state = NORMAL)
self.out_dir_path.delete(1.0, END)
file_name = tkfd.askdirectory(parent=self, title='Select output directory')
self.out_dir_path.insert(INSERT, file_name)
self.out_dir_path.config(state = DISABLED)
def find_directory(self):
folder_path = tkFileDialog.askdirectory(**self.dir_opt)
while not self.is_a_vivaldi_folder(folder_path):
if self.user_close_window(folder_path):
sys.exit(1)
tkMessageBox.showerror("Error searching Vivaldi folder","That isn\'t a Vivaldi folder")
self.dir_opt['initialdir'] = folder_path
folder_path = tkFileDialog.askdirectory(**self.dir_opt)
return folder_path
def tkGUI():
root = tk.Tk();
root.title('Stratec pQCT File Scrubber')
tk.Label (root,
text ="Scrub sensitive patient/participant info from Stratec pQCT files",
font=("Helvetica", 18, "bold"),
).pack(pady=5, padx=10, anchor=tkcnst.W)
tk.Label (root,
text ="* Replace date of birth with the 1st of nearest month\n"+
"* Zero-out patient name field",
font=("Helvetica", 16),
justify=tkcnst.LEFT,
).pack(pady=10, padx=10, anchor=tkcnst.W)
step_label = tk.StringVar()
step_label.set ("\nStep 1: Select folder with Stratec files\n")
tk.Label (root,
textvariable = step_label,
font=("Helvetica", 16, "bold"),
justify=tkcnst.LEFT,
).pack(pady=10, padx=10, anchor=tkcnst.W)
dir_in = tkfd.askdirectory(mustexist=True,title="Select folder with Stratec files")
if not dir_in:
quit()
step_label.set ("\nStep 2: Select folder for scrubbed Stratec files\n")
dir_out = tkfd.askdirectory(mustexist=False,title="Select folder for scrubbed files")
if not dir_out:
sys.exit(0)
step_label.set ("\n'"+dir_in+"' -> '"+dir_out+"'\n")
# update here to get the current size of root
root.update()
progressbar = ttk.Progressbar (orient=tkcnst.HORIZONTAL, length=root.winfo_reqwidth()-40, mode='determinate')
progressbar["value"] = 0
progressbar.pack()
but_frame = tk.Frame(root)
exit_button = tk.Button(but_frame, text="Quit", command=quit)
exit_button.pack(pady=10, padx=10, side=tkcnst.LEFT)
log_button = tk.Button(but_frame, text="View Log", command=view_log)
log_button.pack(pady=10, padx=10, side=tkcnst.LEFT)
but_frame.pack(side=tkcnst.BOTTOM, anchor=tkcnst.W)
# Register an idle task to process the files
idle_task_tk (root, progressbar, process_files (dir_in, dir_out))
root.mainloop()
def browse_for_folder(e):
"""Pull up a folder browsing dialog and dump the resulting path into
the Tkinter.Entry widget e."""
path = tkFileDialog.askdirectory()
if (path != ""): # Unless they hit cancel.
e.delete(0, END)
e.insert(0, path)
def ask_base_dir(self):
"""Selects Baseline Report Folder and Prints it"""
vars.base_dir = tkFileDialog.askdirectory(title="Please Select Baseline Report Directory", initialdir = vars.config.get('Kludge','base_dir'), mustexist = "False")
vars.base_dir = vars.base_dir.replace("/","\\")
self.base_dir_path.set(vars.base_dir)
self.conf_save('base_dir', vars.base_dir)
print ("Baseline Directory " + vars.base_dir)
def outPathBrowse(self):
""" Use the askdirectory tk dialog to get output path. """
self.outPath = tkFileDialog.askdirectory()
if self.outPath:
self.outPath = self.outPath.replace('/', '\\')
self.outEntry.delete(0, tk.END)
self.outEntry.insert(0, self.outPath)
def askdirectory(self):
"""Returns a selected directoryname."""
self.dirname = tkFileDialog.askdirectory(**self.dir_opt)
self.entryVariable.set(self.dirname)
self.buttonView.configure(state=NORMAL)
return self.dirname
def btnOutput(self):
x = tkFileDialog.askdirectory(
mustexist = True,
title = "Select Output Folder",
initialdir = self.outputVar.get())
if x:
self.outputVar.set(x)
def LoadFolder():
global index
global photo
global photolist
global filenames
global factor,scalevalue
scalevalue=100
dirname=""
photolist = []
filenames = []
filetypes = ['*.jpg','*.png','*.gif','*.bmp']
dirname=tkFileDialog.askdirectory(title='Select a directory')
dirname=dirname.replace("\\","/")
dirname=dirname.replace("[","\[")
dirname=dirname.replace("]","\]")
dirname=dirname.replace("\[","[[]")
dirname=dirname.replace("\]","[]]")
if dirname=="":
showwarning("Load Error","You haven't selected a folder")
else:
for type in filetypes:
files = glob.glob(dirname+"//"+type)
for name in files:
name=name.replace("\\","/")
filenames.append(name)
index = 0
factor = 1
NextTen()
def load_dir():
the_dir = tkFileDialog.askdirectory(title=load_dir_text)
if is_label:
label = os.path.basename(the_dir)
else:
label = None
file_list.add_entry_label(the_dir, label)
def main():
root = tk.Tk()
root.withdraw()
rootDir = tkFileDialog.askdirectory() + '\\'
bpDir = '\\Calibration\\BitePlate\\'
palDir = '\\Calibration\\Palate\\'
rawDir = '\\Kinematic\\Raw\\'
corDir = '\\Kinematic\\Corrected\\'
folds = os.listdir(rootDir)
num = '0', '1', '2', '3', '4', '5'
osCol = 86
msCol = 95
decPrec = 4
for f in folds:
if f.startswith(num):
print "Processing " + f + "..."
subFold = rootDir + f + bpDir
bpfiles = [fn for fn in glob.glob(subFold+'/*biteplate*.tsv') if "_BPC" not in fn]
bpfile = bpfiles[-1] # Uses the "last" BP file (in the event of something like bpfile_2.tsv)
indir = rootDir + f + rawDir
outdir = rootDir + f + corDir
files = glob.glob(indir+'/*.tsv')
OS, rot = bpUtils.BiteplateUtils.getRotation(bpfile, osCol, msCol)
processFiles(OS, rot, indir, outdir, decPrec, files)
# Now do the palate traces
indir = rootDir + f + palDir
outdir = indir
files = [fn for fn in glob.glob(indir+'/*.tsv') if "_BPC" not in fn]
processFiles(OS, rot, indir, outdir, decPrec, files)
print f + " done."
def browse(self, widget):
LOG.debug("MainDialog::browse...")
# Tix.DirSelectDialog is deprecated, thus use tk_chooseDirectory
d = tkFileDialog.askdirectory()
# cannot use control variables as the target entry_field is in widget
self.entry_settext(widget, d)
def dialogSelectOutDir(self):
self.outdir = tkFD.askdirectory(initialdir="/",
title="Select output directory")
self.updateInfo()
'''
Utility to create a video from a directory of images
'''
import os
import sys
import cv2
import Tkinter
import tkFileDialog
import tkMessageBox
Tkinter.Tk().withdraw()
sourceDir = tkFileDialog.askdirectory()
destDir = sourceDir + '/' + 'results'
try:
os.mkdir(destDir)
except OSError as e:
if e.errno == 17:
if tkMessageBox.askokcancel(
'Folder already exists',
'The output folder already exists, proceeding may overwrite the files it contains.'
):
pass
else:
print('Exiting ImageBlender')
sys.exit(1)
fileNames = [
sourceDir + '/' + str(f) for f in os.listdir(sourceDir)
if f.endswith('.JPG') or f.endswith('.jpg')
]
def askDir(self):
dirname = filedialog.askdirectory()
self.dir_name.set(dirname)
self.loadDir(dirname)
def browse(self):
dirname = askdirectory()
self.mnt.set(dirname)
self.ent_mnt.delete(0,tk.END)
self.ent_mnt.insert(0,dirname)
#print '\n'.join(OrigPosixPaths)
if args.skipOffline is False:
if args.basic:
ListOfofflineFiles = doesPathExist(OrigPosixPaths)
else:
ListOfofflineFiles = doesPathExist(DecompPosixPaths)
prettySep()
####save reports
print "Check your dock for the python spaceship. Select the folder which will house the reports."
root = Tkinter.Tk()
root.withdraw()
dirname = tkFileDialog.askdirectory(
parent=root,
initialdir='~/Desktop/',
title='A time-stamped subfolder will be created at this location.')
if len(dirname) > 0:
filepaths_ParserReportsDir = dirname + '/' + 'JRAIM_LOGS/FILEPATH_PARSER_REPORTS/' + parsedFilename + timeStampDaFucker(
) + '/'
#print filepaths_ParserReportsDir
else:
print 'Exiting.'
exit()
os.makedirs(filepaths_ParserReportsDir)
print "Writing data to text files...."
initialAssessmentFile = '%s/ListOfFiles_initialAssessment%s.txt' % (
filepaths_ParserReportsDir, timeStampDaFucker())
BrokenApartFile = '%s/ListOfFiles_BrokenApart%s.txt' % (
def getFolderPath(titletext="Please select a folder"):
return tkFileDialog.askdirectory(title=titletext)
Button(master, text='Enter', command=take).grid(row=17,
column=1,
sticky=W,
pady=4)
master.mainloop()
#extracting the number of folders from the list, this is just a quirk of Tkinter
numfolds = numfoldlist[0]
#ask user where exiftool.exe is located. This is neccessary for using the exiftool module.
root = Tkinter.Tk()
currdir = os.getcwd() # current working directory
exiftoolloc = str(
tkFileDialog.askdirectory(
parent=root,
initialdir=currdir,
title='Please select the directory where exiftool.exe is located'))
#empty list for image directories and save directories. There will be the same number of each that corresponds to the number of folders.
origimgdirs = []
savedirs = []
#For every folder user selects image directory of images to be corrected and save directory
h = 1
while h <= numfolds:
root = Tkinter.Tk()
currdir = os.getcwd() # current working directory
orig_img_dir = str(
tkFileDialog.askdirectory(
parent=root,
initialdir=currdir,
def open_output_directory_dialog(self):
filename = tkfd.askdirectory(initialdir=self.initialdir,
title="Select directory")
if filename != '':
self.initialdir = filename
self.output_dirname_var.set(filename)
def browseDirectory(self):
self.targetDir = tkFileDialog.askdirectory()
self.loadFiles()
def load_several_html(cls, text, root):
proc_log = []
if askyesno(u"Загрузить папку", u"Загрузить новую папку?"):
dir_name = askdirectory()
print dir_name
filenames_set = os.listdir(dir_name)
#filenames_set = askopenfilenames()
print filenames_set
text.config(state='normal')
text.delete("1.0", "end")
text.insert("end", u"В обработке...\n")
text.config(state='disabled')
if filenames_set == []:
text.config(state='normal')
text.delete("1.0", "end")
text.insert("end", u"Пожалуйста, выберите файлы.\n")
text.config(state='disabled')
else:
if not os.path.exists(dir_name + '/transliterated/'):
os.mkdir(dir_name + '/transliterated/')
if not os.path.exists(dir_name + '/log/'):
os.mkdir(dir_name + '/log/')
if not os.path.exists(dir_name + '/passed/'):
os.mkdir(dir_name + '/passed/')
passed_files = []
spelling = 1 # SPELLING
for curr_filename in filenames_set:
# print 'CURRENT FILE', curr_filename
if cls.check_transliterated(curr_filename, dir_name):
# print 'IS CHECKED'
META['filename'] = curr_filename
##print meta.filename
name = os.path.splitext(
os.path.basename(META['filename']))[0]
##print meta.res
if META['filename'] == '':
text.config(state='normal')
text.delete("1.0", "end")
text.insert("end",
u"Пожалуйста, выберите файлы.\n")
text.config(state='disabled')
else:
try:
temp_filename = cls.get_temp_in_dir(dir_name)
# print 'START ITERATE'
proc_log.append('START')
new_text, log_data, wrong_log = cls.iterate_root(
temp_filename, root, 0)
# print 'STOP ITERATE'
proc_log.append('STOP')
suffix = os.path.splitext(META['filename'])[1]
META[
'result_name'] = dir_name + '/transliterated/' + name + suffix
with codecs.open(META['result_name'],
'w') as inf:
inf.write(new_text)
log_name = dir_name + '/log/' + name + '_log.txt'
wrong_changes = []
# print 'CREATE LOG NAME'
if log_data:
print 'IS LOG DATA'
log_data = u'\n'.join(log_data)
log_data = log_data.split(u'\n')
# print 'LD'
check_log = [
h.split(u' --> ')[1] for h in log_data
]
# print '-->'
raw_log_forms = [
h.replace(u']',
u'').replace(u'[', u'')
for h in check_log
]
# wrong_changes = []
print 'RAW LOG'
if len(raw_log_forms) < 22000:
check_log_forms = [
u' '.join(raw_log_forms)
]
print 'CREATE LOG FORMS'
else:
check_log_forms = []
tmp_clf = []
for o, uu in enumerate(raw_log_forms):
if o != 0 and not o % 22000:
check_log_forms.append(
u' '.join(tmp_clf))
tmp_clf = []
tmp_clf.append(uu)
if tmp_clf:
check_log_forms.append(
u' '.join(tmp_clf))
with codecs.open('log_forms', 'w',
'utf-8') as chlf:
chlf.write(u'\n'.join(check_log_forms))
print 'CHECK LOG'
if spelling:
print 'SPELLING'
spelled_raw = []
for chlf in check_log_forms:
print 'PART LOG'
cmd = "echo " + chlf + " | hunspell -d ru_Ru"
p = subprocess.Popen(
cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True,
executable="/bin/bash")
spelled, err_sp = p.communicate()
spelled_parts = spelled.decode(
'utf-8').split('\n')[1:][:-2]
spelled_raw += spelled_parts
print 'SPELLED ALL PARTS'
# with codecs.open('spell_test.txt', 'w', 'utf-8') as spw:
# spw.write(u'\n'.join(spelled))
# with codecs.open('log_test_2.txt', 'w', 'utf-8') as ss:
# ss.write(u'\n'.join(log_data))
# for j, sp in enumerate(spelled):
# if sp[0] == u'&':
# print j, sp, u'=', log_data[j]
# wrong_changes.append(log_data[j])
# log_data[j] = log_data[j] + u' *'
# print 'DECODED SPELLED'
spelled = []
for s in spelled_raw:
if s.strip() != u'':
spelled.append(s)
# print 'GET SPELLED LIST'
gap = 0
num_gap = 0
for j, sp in enumerate(log_data):
prev_pos = j + gap - num_gap
# if j == 31:
# pass
# print 'IM IN', j, sp, gap
# print 'DATA', j + gap, len(spelled)
curr_word = sp.split(u' --> ')[1]
# if curr_word == u'Дон-Кихоте':
# pass
if re.search(
u'^[0-9\-]+$', curr_word):
num_gap += 1
continue
if j + gap - num_gap >= len(
spelled):
break
# print 'NOW SPELL'
# print 'THIS', j + gap - num_gap, spelled[j + gap - num_gap]
# print u'%%%%'.join(spelled[686:690])
if spelled[j + gap -
num_gap][0] == u'&':
print j, spelled[
j + gap -
num_gap], u'=', log_data[j]
spell_ans = u' '.join(
spelled[j + gap -
num_gap].split(
u':')
[0].split(u' ')[1:-2])
# wrong_changes.append(log_data[j])
wrong_changes.append(spell_ans)
log_data[
j] = log_data[j] + u' *'
# print 'NOW HYP'
if u' ' in curr_word:
curr_arr_space = curr_word.split(
u' ')
gap += len(
re.findall(
u' ', curr_word))
else:
curr_arr_space = [curr_word]
curr_arr = []
for m, curr_p in enumerate(
curr_arr_space):
if u'-' in curr_p:
gap += len(
re.findall(
u'-', curr_p))
curr_p = curr_p.split(u'-')
if curr_p == [u'', u'']:
gap -= 1
continue
for cwp in curr_p:
if re.search(
u'^[0-9]+$',
cwp
) or cwp == u'':
gap -= 1
if cwp != u'':
curr_arr.append(
cwp)
else:
curr_arr.append(curr_p)
# print 'CHECK -'
new_curr_arr = []
for m, curr_p in enumerate(
curr_arr):
if re.search(u'[0-9]', curr_p):
# new_curr_arr = []
# for cwp in curr_arr:
tmp_cwp = re.split(
u'[0-9]+', curr_p)
if tmp_cwp[0] == u'':
tmp_cwp = tmp_cwp[1:]
if tmp_cwp and tmp_cwp[
-1] == u'':
tmp_cwp = tmp_cwp[:-1]
if tmp_cwp:
new_curr_arr += tmp_cwp
if len(new_curr_arr) > len(
curr_arr):
num_gap += len(
new_curr_arr
) - len(curr_arr)
else:
new_curr_arr.append(curr_p)
# print 'CHECK NUM'
if j + gap - num_gap > prev_pos:
# print 'IS DIFF'
# diff = j + gap - num_gap - prev_pos
try_pos = 1
while prev_pos + try_pos < j + gap - num_gap + 1:
if spelled[prev_pos +
try_pos][
0] == u'&':
# print j, spelled[prev_pos + try_pos], u'=', log_data[j]
wrong_changes.append(
log_data[j])
log_data[j] = log_data[
j] + u' *'
break
try_pos += 1
# print 'CHECK DIFF'
print 'SPELLED'
with codecs.open(log_name, 'w',
'utf-8') as logf:
logf.write(u'\n'.join(log_data))
# logf.write(log_data)
print 'SAVE LOG'
wrong_log_name = dir_name + '/log/' + name + '_err_spelled.txt'
with codecs.open(wrong_log_name, 'w',
'utf-8') as wrf:
wrf.write(u'\n'.join(wrong_changes))
print 'SAVE WRONG'
except:
#print 'PASSED', meta.filename
if proc_log[-1] == 'STOP':
try:
with codecs.open(
'err_in_spell', 'a',
'utf-8') as eis:
eis.write(META['filename'])
eis.write(u'\n')
except:
try:
with codecs.open(
'err_in_spell', 'a',
'utf-8') as eis:
eis.write(
META['filename'].decode(
'utf-8'))
eis.write(u'\n')
except:
pass
elif proc_log[-1] == 'START':
try:
with codecs.open(
'err_in_struct', 'a',
'utf-8') as eis:
eis.write(META['filename'])
eis.write(u'\n')
except:
try:
with codecs.open(
'err_in_struct', 'a',
'utf-8') as eis:
eis.write(
META['filename'].decode(
'utf-8'))
eis.write(u'\n')
except:
pass
passed_files.append(META['filename'])
else:
# passed_files.append(META['filename'])
print 'DIDNT CHECKED'
passed_files.append(curr_filename)
text.config(state='normal')
text.delete('1.0', 'end')
text.insert('end', u'\nВыполнено\n')
text.configure(cursor='arrow')
text.config(state='disabled')
SaveText.save_passed(passed_files, dir_name)
def get_sdir(self):
subject_directory = tkFileDialog.askdirectory()
self.sdir_label_text.set(subject_directory)
def click_save(self):
filename = filedialog.askdirectory(initialdir='~/')
self.save_path.config(text=filename)
mat_answer = scipy.io.loadmat(filename_path)
answer_sheet = mat_answer['answer_sheet']
# load data_matrix from each recording site
# for each file
# divided to 2 parts (80% training, 20% testing)
# do this for n times
# each time 80% used to train SVM
# test this SVM on the 20% data
# output the accuracy each time and calculate average
file_path = os.path.dirname(os.path.realpath(__file__))
root = Tkinter.Tk()
root.withdraw()
dirname = tkFileDialog.askdirectory(parent=root,
initialdir=file_path,
title='Please select a directory')
filename_list = []
# path to save all jj of 100 classifilers
jj_path = 'C:\\Users\\mz86\\Desktop\\fNIRS ML\\trained_classifiers\\100_exp1_MNN'
# for jj times repeat train 100 classifier on each recording site.
for jj in range(0, 1):
# for this jj save trained 100 clasifier at
jj_path_each = jj_path + '\\' + str(jj)
# repeat this whole process k times
# to aclculate the averrage accuracy
def button_setrecdir(self):
path = tkFileDialog.askdirectory(
initialdir=".", title='Select directory for recosnstructions')
self.e[5].delete(0, Tkinter.END)
self.e[5].insert(0, path)
else:
zip.write(os.path.join(dirpath, file),
os.path.join(dirpath[len(path):], file))
except Exception, e:
print(" Error adding {}: {}".format(file, e))
return None
try:
root = Tkinter.Tk()
root.withdraw()
root.attributes('-topmost', True)
getGDBLoc = tkFileDialog.askdirectory(
parent=root,
initialdir="C:",
title='Select the folder which contains the GDBs to be zipped')
root.attributes('-topmost', False)
wkPath = os.path.abspath(getGDBLoc).replace("\\", "/")
root.destroy()
# Create the zip file for writing compressed data. In some rare instances, the ZIP_DEFLATED constant may be unavailable and the
# ZIP_STORED constant is used instead. When ZIP_STORED is used, the zip file does not contain compressed data, resulting in large zip files.
for fldr in os.listdir(wkPath):
if fldr.endswith('.gdb'):
outfile = fldr + ".zip"
try:
zip = zipfile.ZipFile(os.path.join(wkPath, outfile), 'w',
zipfile.ZIP_DEFLATED)
zipws(os.path.join(wkPath, fldr), zip, False)
zip.close()
def open_kml_server_preview_directory_dialog(self):
filename = tkfd.askdirectory(initialdir=self.initialdir,
title="Select directory")
if filename != '':
self.initialdir = filename
self.kml_server_preview_directory_var.set(filename)
def dirnameDialog_text(self, text):
fl = tkFileDialog.askdirectory(initialdir=text.get())
if fl != '':
self.reset_entry(text, fl)
def selectgraceformatteddatadir(self):
self.formatteddatapath = tkFileDialog.askdirectory(
initialdir="/", title="Select GRACE formatted Data Directory")
self.inputgracedirtxtfield.delete(1.0, tk.END)
self.inputgracedirtxtfield.insert(tk.END, self.formatteddatapath)
def open_photo(self):
self.backup_path = self.path.get()
path_ = tkFileDialog.askdirectory()
self.var_msg.set("Importing images... This may take awhile =) ")
self.path.set(path_)
print("folder path: %s" % self.path.get())
# handle error when user click 'cancel' button on the import image window
if self.path.get() == '':
self.var_msg.set("Please select an image folder.")
print("Please select an image folder.")
self.path.set(self.backup_path)
else:
self.file_ls = [
] # image list: [(<Tkinter.Checkbutton instance>,<Tkinter.IntVar instance>),......]
self.file_chosen_ls = [
] # image data list: [<Tkinter.Checkbutton instance>,......]
self.datetime_ls = []
self.image = []
self.photo = []
# delete photos on GUI
self.frame_in2.destroy()
self.frame_in2 = Tk.Frame(self.canvas)
# self.canvas.create_window((0, 0), window = self.frame_in2, anchor="center", height="25c", width="15c")
# self.frame_in2.grid()
self.canvas.create_window((0, 0),
window=self.frame_in2,
anchor='nw')
self.frame_in2.bind("<Configure>", self.my_canvas)
# Handle No. of rows of photos based on image frame width
no_row = self.get_row()
col = 0
row = 0
for file_name in os.listdir(self.path.get()):
global image, photo
if file_name.endswith(".jpg") or file_name.endswith(".jpeg"):
self.image.insert(
0,
Image.open(os.path.join(
self.path.get(),
file_name)).resize((self.image_width,
int(self.image_width * 0.75))))
self.photo.insert(0, ImageTk.PhotoImage(self.image[0]))
var = Tk.IntVar()
c1 = Tk.Checkbutton(self.frame_in2,
text=file_name,
image=self.photo[0],
variable=var,
onvalue=1,
offvalue=0,
width=self.cb_width)
c1.grid(row=row, column=col)
# c1.pack()
col += 1
if col >= no_row:
row += 1
col = 0
self.file_ls.append((c1, var))
# handle no image folder
if len(self.file_ls) == 0:
self.var_msg.set("No jpg or jpeg file in %s." %
self.path.get())
else:
self.var_msg.set("Imported " + str(len(self.file_ls)) +
" images successfully from " +
str(self.path.get()) + ".")
self.db_name = self.getDbName(self.path.get())
# Create directory if it is not exist
if os.path.isdir("../database/data_" + self.db_name) == False:
os.mkdir("../database/data_" + self.db_name, 0755)
print "Path is created"
self.db_link = "../database/data_" + self.db_name + "/" + self.db_name + '.db'
with sqlite3.connect(self.db_link) as db:
cur = db.cursor()
# Create table if it is a new database
if db is not None:
self.create_table(
db, self.sql_create_table
) # only execute this line when db is a new database
print("Created a new database: %s" % self.db_name +
'.db')
self.var_msg.set("Created a new database: %s" %
self.db_name + '.db')
else:
print("Error! cannot create the database connection.")
for x in self.file_ls:
f = x[0]
name = f.cget("text")
cur.execute(
"SELECT id FROM attributes WHERE file = (?)",
(name, ))
row = cur.fetchall()
# If picture is already recorded in database
if len(row) != 0:
f.configure(bg="tomato")
normal_samples_gene_expressions[gene_name] = []
for sample_id in gene_expression.get_samples_list():
sample_gene_expression_value = gene_expression.get_gene_exp_matrix_dataframe()[sample_id][gene_name]
if gene_expression.get_sample_tissue_types_dict()[sample_id] == constants.SAMPLE_TYPE_TUMOR:
tumor_samples_gene_expressions[gene_name].append(sample_gene_expression_value)
elif gene_expression.get_sample_tissue_types_dict()[sample_id] == constants.SAMPLE_TYPE_NORMAL:
normal_samples_gene_expressions[gene_name].append(sample_gene_expression_value)
if float(np.mean(np.array(normal_samples_gene_expressions[gene_name]))) == 0.0:
avg_gene_exp_ratio[gene_name] = "n/a"
else:
avg_gene_exp_ratio[gene_name] = float(np.mean(np.array(tumor_samples_gene_expressions[gene_name]))) / \
float(np.mean(np.array(normal_samples_gene_expressions[gene_name])))
print("\nFinished calculating average gene expression value ratio\n\n")
# Write .csv files
print("---> Please select the directory to which you want to save the analysis results.gene expression file downloaded from UCSC Xena Browser <---\n\n")
save_dir = tkFileDialog.askdirectory()
root.update()
if save_dir is None:
exit()
print("Started writing data to .csv files")
summary_file = save_dir + "/results/analysis.csv"
raw_gene_exp_file = save_dir + "/results/gene_expressions.csv"
# Create the files
if not os.path.exists(os.path.dirname(summary_file)):
try:
os.makedirs(os.path.dirname(summary_file))
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise
if not os.path.exists(os.path.dirname(raw_gene_exp_file)):
try:
def file_browse(self):
self.dir_name = tkFileDialog.askdirectory(
initialdir="/", title='Choose a target directory')
pe_name = str(os.path.normpath(self.dir_name))
# print pe_name
self.fill_path(str(pe_name))
def dir_open():
dir_path = tkFileDialog.askdirectory()
e1.delete(0, END)
e1.insert(0, dir_path)
print('Writing processed data to {0}'.format(outfile))
alldat.to_csv(outfile, index=False)
pstc_df = get_pstc_data(datadir)
pstc_df = pstc_df.astype({"Subject": str, "Session": str})
blink_df = blink_df.astype({"Subject": str, "Session": str})
pstc_df = pd.merge(pstc_df, blink_df, on=['Subject','Session','OddballSession'])
pstc_outfile = os.path.join(datadir, 'oddball_group_pstc_' + tstamp + '.png')
plot_group_pstc(pstc_df, pstc_outfile)
if __name__ == '__main__':
if len(sys.argv) == 1:
print('USAGE: {} <data directory> '.format(os.path.basename(sys.argv[0])))
print("""Searches for datafiles created by oddball_proc_subject.py for use as input.
This includes:
<session>-<subject>_SessionData.csv
<session>-<subject>_PSTCdata.csv
<session>-<subject>_BlinkPct.json
<session>-<subject>_GLMresults.json
Calculates subject level measures of pupil dilation and contrast to noise ratios.
Plots group level PTSC. Output can be used for statistical analysis.""")
root = tkinter.Tk()
root.withdraw()
# Select folder containing all data to process
datadir = filedialog.askdirectory(title='Choose directory containing subject data')
proc_group(datadir)
else:
datadir = sys.argv[1]
proc_group(datadir)
def SelectFolderDialog():
Tk().withdraw()
folder = askdirectory()
return folder
def browse_button(entry):
filename = tkFileDialog.askdirectory()
entry.insert(0, filename)
def chooseDir(self, parent, controller, place_holder, message): current_dir = os.getcwd() parent.update() chosen_dir = tkFileDialog.askdirectory(parent=self, initialdir = current_dir, title='Select the location of ' + message) place_holder.set(chosen_dir)
def output_askdirectory(self):
select_dir = tkFileDialog.askdirectory()
self.output_directory.set(select_dir)
return select_dir
def Execute(self):
if self.Image == None:
if self.Input == None:
self.PrintError('Error: no Image.')
self.Image = self.Input
extensionFormats = {
'vti': 'vtkxml',
'vtkxml': 'vtkxml',
'vtk': 'vtk',
'mhd': 'meta',
'mha': 'meta',
'tif': 'tiff',
'png': 'png',
'dat': 'pointdata'
}
if self.OutputFileName == 'BROWSER':
import tkFileDialog
initialDir = '.'
self.OutputFileName = tkFileDialog.asksaveasfilename(
title="Output image", initialdir=initialDir)
if not self.OutputFileName:
self.PrintError('Error: no OutputFileName.')
if self.OutputDirectoryName == 'BROWSER':
import tkFileDialog
initialDir = '.'
self.OutputDirectoryName = tkFileDialog.askdirectory(
title="Output directory", initialdir=initialDir)
if not self.OutputDirectoryName:
self.PrintError('Error: no OutputDirectoryName.')
if self.GuessFormat and self.OutputFileName and not self.Format:
import os.path
extension = os.path.splitext(self.OutputFileName)[1]
if extension:
extension = extension[1:]
if extension in extensionFormats.keys():
self.Format = extensionFormats[extension]
if self.PixelRepresentation != '':
cast = vtk.vtkImageCast()
cast.SetInput(self.Image)
if self.PixelRepresentation == 'double':
cast.SetOutputScalarTypeToDouble()
elif self.PixelRepresentation == 'float':
cast.SetOutputScalarTypeToFloat()
elif self.PixelRepresentation == 'short':
cast.SetOutputScalarTypeToShort()
else:
self.PrintError('Error: unsupported pixel representation ' +
self.PixelRepresentation + '.')
cast.Update()
self.Image = cast.GetOutput()
if self.UseITKIO and self.Format not in [
'vtkxml', 'tiff', 'png', 'dat'
]:
self.WriteITKIO()
else:
if (self.Format == 'vtkxml'):
self.WriteVTKXMLImageFile()
elif (self.Format == 'vtk'):
self.WriteVTKImageFile()
elif (self.Format == 'meta'):
self.WriteMetaImageFile()
elif (self.Format == 'png'):
self.WritePNGImageFile()
elif (self.Format == 'tiff'):
self.WriteTIFFImageFile()
elif (self.Format == 'pointdata'):
self.WritePointDataImageFile()
else:
self.PrintError('Error: unsupported format ' + self.Format +
'.')
def dialog_for_lecture_path():
classes_dir = rwkos.FindFullPath('siue/classes')
outpath = tkFileDialog.askdirectory(initialdir=classes_dir)
outpath = force_seps(outpath)
return outpath
