def opencsv(self, name):
# Return if the csv object was not set.
# if self.trackscsv == None: return None TODO: some errorchecking for false csv input.
# Open the csv file and return it as ResultsTable object.
try:
csv = IJ.getFilePath("Choose the {} file".format(name))
if csv.endswith(".csv"):
rt = ResultsTable.open(csv)
else:
IJ.log("{} was not a .csv file".format(csv))
raise ValueError
columns = rt.getHeadings()
table = [{column: rt.getValue(column, row)
for column in columns} for row in range(rt.size())]
if rt.columnExists("Label"):
for i in range(len(table)):
table[i]["Label"] = rt.getStringValue("Label", i)
IJ.log("Read {} rows in {}.".format(len(table), name))
return table
except Exception as ex:
IJ.log("Something in opencsv() went wrong: {}".format(
type(ex).__name__, ex.args))
def opencsv():
"""Simply imports .csv file in ImageJ.
Ask the user for the location of a .csv file.
Returns:
A ResultsTable object from the input file.
"""
csv = IJ.getFilePath("Choose a .csv file")
# Open the csv file and return it as ResultsTable object.
try:
if csv.endswith(".csv"):
res = ResultsTable.open(csv)
return res
else:
raise TypeError()
except TypeError:
IJ.log("The chosen file was not a .csv file.")
except Exception as ex:
IJ.log("Something in opencsv() went wrong: {}".format(type(ex).__name__, ex.args))
# Process list of images
for (counter, f) in enumerate(files):
# Display progress
IJ.showStatus("Processing file "+ str(counter+1) +"/"+ str(len(files)))
# Open each image and process it
imp = IJ.openImage(f)
myRoutines(imp)
# Save processed image in out_dir (enforcing .tif extension)
newpath = os.path.splitext(out_dir + imp.getTitle())[0] +".tif"
IJ.saveAsTiff(imp, newpath)
imp.close()
# Log paths of processed files
csvWriter.writerow([f, newpath])
# Display CSV log
csvFile.close()
rt = ResultsTable.open(csvPath)
rt.show("_ProcessedFileList.csv")
# Proudly inform that processing terminated
if IJ.showMessageWithCancel("All done","Reveal output directory?"):
Utils.revealFile(out_dir);
else:
# Inform no filtered files were found
IJ.error("No matches for the selected extension(s).")
# IJ BAR: https://github.com/tferr/Scripts#scripts
#
# Imports numeric values copied to the clipboard into the Results table. It is
# now deprecated. It was of utility prior to BAR v1.1.7, when BARs that analyzed
# tabular data could only read values from the main IJ "Results" table. It is
# included here as a programming example.
#
# Requirements: Requires BAR_-XX.jar to be installed in the plugins folder of IJ
#
# NB: When copying data from withing IJ (e.g., lists from histograms or plot profiles),
# Use Edit>Options>Input/Output... to specify if column headers/row numbers should be
# copied to the clipboard
import os, tempfile
from bar import Utils as barUtils
from ij import IJ
from ij.plugin.filter import Analyzer
import ij.measure.ResultsTable as RT
fd, path = tempfile.mkstemp()
try:
os.write(fd, barUtils.getClipboardText())
os.close(fd)
rt = RT.open(path) #IOException if getClipboardText()==""
if Analyzer.resetCounter():
rt.show("Results")
except:
IJ.showMessage("Could not place clipboard into Results table.")
finally:
os.remove(path)
# IJ BAR: https://github.com/tferr/Scripts#scripts
#
# Imports numeric values copied to the clipboard into the Results table. Useful, since
# BARs that analyze tabular data can only read values from the main IJ "Results" table
#
# Requirements: Requires BAR_-XX.jar to be installed in the plugins folder of IJ
#
# NB: When copying data from withing IJ (e.g., lists from histograms or plot profiles),
# Use Edit>Options>Input/Output... to specify if column headers/row numbers should be
# copied to the clipboard
import os, sys, tempfile
from bar import Utils as barUtils
from ij import IJ
from ij.plugin.filter import Analyzer
import ij.measure.ResultsTable as RT
fd, path = tempfile.mkstemp()
try:
os.write(fd, barUtils.getClipboardText())
os.close(fd)
rt = RT.open(path) #IOException if getClipboardText()==""
if Analyzer.resetCounter():
rt.show("Results")
except:
IJ.error("Could not place clipboard into Results table.")
finally:
os.remove(path)
image_two = HyperStackConverter.toHyperStack(image,2,z_slices,1) image = CompositeImage(image_two) image.show() rt = run_comdet(image) rt.save(directory+"/"+filename+"_results.csv" ) image = IJ.getImage() if auto_cell: mask = generate_mask(image_green, auto_cell_thresh) fs = FileSaver(mask) filepath = directory + "/" + filename + "_mask.tiff" fs.saveAsTiff(filepath) rest = ResultsTable.open(directory+"/"+filename+"_results.csv") #print(rest.getColumnHeadings()) remove_outside_cell(rest,mask) rest.save(directory+"/"+filename+"_results.csv" ) else: rest = rt image.setDimensions(2, z_slices, 1) image.setOpenAsHyperStack(True)
image_two = HyperStackConverter.toHyperStack(image, 2, z_slices, 1)
image = CompositeImage(image_two)
image.show()
rt = run_comdet(image)
rt.save(directory + "/" + filename + "_results.csv")
image = IJ.getImage()
if auto_cell:
mask = generate_mask(image_green, auto_cell_thresh)
fs = FileSaver(mask)
filepath = directory + "/" + filename + "_mask.tiff"
fs.saveAsTiff(filepath)
rest = ResultsTable.open(directory + "/" + filename + "_results.csv")
#print(rest.getColumnHeadings())
remove_outside_cell(rest, mask)
rest.save(directory + "/" + filename + "_results.csv")
else:
rest = rt
image.setDimensions(2, z_slices, 1)
image.setOpenAsHyperStack(True)
print(image.isHyperStack(), image.getNChannels(), image.getOverlay())
#image.flattenStack()
image.show()
fs = FileSaver(image)
filepath = directory + "/" + filename + "_coloc.tiff"