def run():
bPrintLog(' ', 0)
bPrintLog('=====================================', 0)
bPrintLog('Running bAlign_Batch_v7', 0)
bPrintLog('=====================================', 0)
if len(sys.argv) < 2:
print " We need a hard-drive folder with .tif stacks as input"
print " Usage: ./fiji-macosx bALign_Batch_7 <full-path-to-folder>/"
# Prompt user for a folder
sourceFolder = DirectoryChooser(
"Please Choose A Directory Of .tif Files").getDirectory()
if not sourceFolder:
return 0
strippedFolder = sourceFolder.replace(' ', '')
if sourceFolder != strippedFolder:
print 'found a space in specified path. Pease remove spaces and try again.'
print 'path:', sourceFolder
errorDialog = GenericDialog('Align Batch 7 Options')
errorDialog.addMessage('bAlignBatch7 Error !!!')
errorDialog.addMessage('There can not be any spaces in the path.')
errorDialog.addMessage('Please remove spaces and try again.')
errorDialog.addMessage('Offending path is:')
errorDialog.addMessage(sourceFolder)
errorDialog.showDialog()
return 0
else:
sourceFolder = sys.argv[1] #assuming it ends in '/'
if not os.path.isdir(sourceFolder):
bPrintLog('\nERROR: run() did not find folder: ' + sourceFolder + '\n',
0)
return 0
if (Options(sourceFolder)):
runOneFolder(sourceFolder)
bPrintLog('=====================================', 0)
bPrintLog('Done bAlign_Batch_v7', 0)
bPrintLog('=====================================', 0)
bPrintLog(' ', 0)
def run():
bPrintLog(' ', 0)
bPrintLog('=====================================', 0)
bPrintLog('Running bAlign_Batch_v7', 0)
bPrintLog('=====================================', 0)
if len(sys.argv) < 2:
print " We need a hard-drive folder with .tif stacks as input"
print " Usage: ./fiji-macosx bALign_Batch_7 <full-path-to-folder>/"
# Prompt user for a folder
sourceFolder = DirectoryChooser("Please Choose A Directory Of .tif Files").getDirectory()
if not sourceFolder:
return 0
strippedFolder = sourceFolder.replace(' ', '')
if sourceFolder != strippedFolder:
print 'found a space in specified path. Pease remove spaces and try again.'
print 'path:', sourceFolder
errorDialog = GenericDialog('Align Batch 7 Options')
errorDialog.addMessage('bAlignBatch7 Error !!!')
errorDialog.addMessage('There can not be any spaces in the path.')
errorDialog.addMessage('Please remove spaces and try again.')
errorDialog.addMessage('Offending path is:')
errorDialog.addMessage(sourceFolder)
errorDialog.showDialog()
return 0
else:
sourceFolder = sys.argv[1] #assuming it ends in '/'
if not os.path.isdir(sourceFolder):
bPrintLog('\nERROR: run() did not find folder: ' + sourceFolder + '\n',0)
return 0
if (Options(sourceFolder)):
runOneFolder(sourceFolder)
bPrintLog('=====================================', 0)
bPrintLog('Done bAlign_Batch_v7', 0)
bPrintLog('=====================================', 0)
bPrintLog(' ', 0)
psgd.showDialog()
choose = psgd.getNextNumber()
choice = psgd.getCheckboxes().get(0).getState()
#open a tab separated txt file with one column Frame selected
if choice == 1:
choose = 0
IJ.run("Table... ", "open=")
frametable = WM.getWindow("selected_frames.txt")
meta = frametable.getTextPanel()
metaRT = TP.getResultsTable(meta)
# Choose a directory
directory_load = DirectoryChooser(
"Select the directory of your files").getDirectory()
directory_load = directory_load.replace("\\", "/")
# get a list of all files in the directory
dList = os.listdir(directory_load)
# set a counter to 1
n = 1
for i in dList:
dL = directory_load + "/" + str(i)
#consider only files with .ome file ending
if ".ome" in dL:
#open the images as virtual stack
imp = IJ.run(
"Bio-Formats", "open=[" + dL +
"] color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT use_virtual_stack"
#If okay was clicked in the 6D_processor dialog the checkboxes are read and an output is created
if gd.wasOKed():
if checkbox1 == True or checkbox3 == True or checkbox2 == True:
#Output option 1 is making a subset of loops, that are then exported as XYTC.tiff
if checkbox1 == True:
if choiceIm == True:
greenwindow = WM.getWindow("green_" + title)
WM.setCurrentWindow(greenwindow)
impDir = IJ.getDirectory("current")
impDir = impDir.replace("\\", "/")
impDir = impDir + title
pat = title
directory_save_subset = DirectoryChooser(
"Select the directory to save the files").getDirectory()
directory_save_subset = directory_save_subset.replace(
"\\", "/")
MakeSubset(impDir, directory_save_subset, ch, frames, zplanes,
loops, total, pat, title, imp2)
#Output option 2 is exporting all the dataset to XYTC.tiff
if checkbox2 == True or checkbox3 == True:
directory_save_xytc = DirectoryChooser(
"Select the directory to save the files").getDirectory()
directory_save_xytc = directory_save_xytc.replace("\\", "/")
pat = title
XYTCZL(impDir, directory_save_xytc, ch, frames, zplanes, loops,
total, pat, title)
#Output option 3 is additionally creating a csv-file with information for matlab BeatSync
if checkbox3 == True:
directory_save = DirectoryChooser(
"Select the directory to save the files").getDirectory()
