def createExportDir(self, export_name):
""" Creates export directory
Parameters
----------
export_name : str
Name of folder. i.e. <img directory>/<export_name>
Returns
-------
current_export_dir : str, path-like
Path to export directory <img_directory>/<export_name>/<current_datetime>
"""
IJ.selectWindow(self.ref_image.ID) # make ref image active window
current_datetime = datetime.datetime.now().strftime("%Y%m%d_%H%M")
export_dir = os.path.join(IJ.getDir("image"), export_name)
if os.path.isdir(export_dir) == False:
IJ.log("Created export directory: " + export_dir)
os.mkdir(export_dir)
current_export_dir = os.path.join(export_dir, current_datetime)
os.mkdir(current_export_dir)
IJ.log("Currently exporting to: " + current_export_dir)
return current_export_dir
def __init__(self, uniqueFileName, outputFolder):
self.uniqueID = uniqueFileName[:-4]
self.outputFolder = str(outputFolder)
elapsedTime = (datetime.now() -
datetime.fromtimestamp(0)).total_seconds()
elapsedTimeStr = str(elapsedTime)
self.downloadsFolder = join(IJ.getDir("downloads"),
"SpeckleResults" + self.outputFolder)
if not exists(self.downloadsFolder):
os.mkdir(self.downloadsFolder)
def openedImagesmain(channel1, channel2, ignoreString, primarySize,
primaryImageThresh, secondaryImageThresh):
def writeTablesToCSV(id, roiOut, speckleOut):
try:
#append your labels to them before they're written
identifier = id[:-4]
speckleOut_ = RTC.appendColToFront(identifier, speckleOut)
roiOut_ = RTC.appendColToFront(identifier, roiOut)
#save the tables to csvs -- they will append to a currently existing csv
#or create a new one
Saves.table2CSV("speckleOutput.csv", speckleOut_)
Saves.table2CSV("AnalysisOutput.csv", roiOut_)
print("finished writing tables to csvs.")
except:
print("failed to write to csvs.")
finally:
print("")
#Begin
try:
RTC = ResultsTableToCSV(channel1, channel2, ignoreString)
primary, secondary, images = RTC.getOpenImageNames()
Binarize(primaryImageThresh, secondaryImageThresh, primary, secondary)
speckleInputs = "primary=[{}] secondary=[{}] " \
"redirect=None min_primary_size={} min_secondary_size=0.00000 " \
"show=none exclude speckle statistic secondary_object"
IJ.run("Speckle Inspector",
speckleInputs.format(primary, secondary, primarySize))
Saves = SaveStuff(primary)
Saves.saveLogs()
#Saves.saveNewImages(images)
Saves.saveAllImages(images)
speckleTableName = "Speckle List " + primary
roiTableName = "Roi Analysis"
roiOut = RTC.roiAnalysisToWrite(roiTableName)
speckleOut = RTC.readResultsTablesOfNumbers(speckleTableName)
WindowManager.closeAllWindows()
fijiDir = IJ.getDir("imagej")
fijiScriptsDir = join(fijiDir, "scripts")
writeTablesToCSV(primary, roiOut, speckleOut)
IJ.open(join(fijiScriptsDir, "SmootherSpeckling.py"))
print("script completed successfully.")
except:
print("sorry, the script broke :/")
finally:
print("")
IJ.run("Close")
c=1
for series in loc2:
out_path=filepath1 + "/"+name+"Scene_" + str(c) + ".tif"
imp=getImageSeries(imps, series)
imp.show()
IJ.run("RGB Color")
imp.close()
IJ.saveAs("tiff", out_path)
IJ.run("Close")
c+=1
czireader.close()
# clear the console automatically when not in headless mode
uiService.getDefaultUI().getConsolePane().clear()
inputDir = IJ.getDir("Choose input Directory")
#only grabs files in case there are any folders in the directory
#https://stackoverflow.com/questions/11968976/list-files-in-only-the-current-directory
dir_array1 = [f for f in os.listdir(inputDir) if os.path.isfile(os.path.join(inputDir,f))]
#does not generate a tiff file or folder for the thumbnail pictures of the preview and label
dir_array=[f for f in dir_array1 if "pt" not in f]
log.info(dir_array1)
log.info(dir_array)
dir_length = len(dir_array)
#create an output directory inside the folder with all the other ones
for i,image in enumerate(dir_array):
from ij import IJ
import os
path = IJ.getDir("Choose a Directory")
c = 0
for f in os.listdir(path):
try:
ext = f.split('.')[-1]
ch = f.split('.')[-2]
except:
continue
if ext == 'tif' and ch == 'UV':
print f, " is a UV channel"
img = IJ.open(''.join([path, f]))
#IJ.setAutoThreshold(img, "Default dark")
IJ.run("8-bit")
IJ.setThreshold(255, 255)
IJ.run("Close")
c += 1
if c >= 5:
break
