def import_multiple_rois(roi_files):
rois = [f.getPath() for f in roi_files if f.exists() and f.getName().lower().endswith("roi")]
opener = Opener()
rm = RoiManager.getRoiManager()
if not rm.getInstance():
rm.reset()
[rm.addRoi(opener.openRoi(r)) for r in rois]
def normalized_roi_length(roi_path, pixel_scaling, normalization_fn=None):
'''
Returns the scaled measure of the input roi performing the normalization
function if provided.
'''
opener = Opener()
roi = opener.openRoi(roi_path)
scaled_measure = roi.getLength() / pixel_scaling
if callable(normalization_fn):
return normalization_fn(scaled_measure)
return measure
def batch_profile_from_threshold(batch_parameters):
'''
Thresholds the desired channel using the threshold method specified and saves the
roi profile in the csv_output.
Rois will be set to the width in pixels specified by stroke_width.
Provide a batch parameters dict to operate on images.
WIP:
PUT A BETTER ALGO IN PLACE TO DETERMINE THE CORRECT ROI TO USE.
'''
from ij.io import Opener
from IBPlib.ij.Utils.Files import buildList
opener = Opener()
rois_folder, csvs_folder = setup_output_folders(batch_parameters.get("output_folder"))
IJ.log("Plotting profiles...")
for i, img in enumerate(batch_parameters.get("analysed_images")):
progress = "{0}/{1}".format(i+1, len(batch_parameters.get("analysed_images")))
IJ.log("\n# Progress: {0}\n".format(progress))
imp = imageloader(img)
#title = os.path.basename(os.path.splitext(img)[0])
title = os.path.basename(img)
IJ.log("\nMeasuring -> {0}".format(title))
rois_path_list = buildList(rois_folder, extension=".roi")
rois = [opener.openRoi(roi) for roi in rois_path_list if roi.find(title) > 0]
if not rois:
IJ.log("## No rois found for {0}".format(title))
if not profile_from_threshold(imp, batch_parameters.get("analysis_ch"),
rois, batch_parameters.get("stroke_width"),
batch_parameters.get("th_method"), csvs_folder):
IJ.log("Batch run canceled.")
return
IJ.log("Done ...")
IJ.log("Results stored in '{0}'".format(csvs_folder))
rois_path_list = buildList(rois_folder, extension=".roi")
rois = [opener.openRoi(roi) for roi in rois_path_list if roi.find(title) > 0]
if not rois:
IJ.log("## No rois found for {0}".format(title))
if not profile_from_threshold(imp, batch_parameters.get("analysis_ch"),
rois, batch_parameters.get("stroke_width"),
batch_parameters.get("th_method"), csvs_folder):
IJ.log("Batch run canceled.")
return
IJ.log("Done ...")
IJ.log("Results stored in '{0}'".format(csvs_folder))
if __name__ in ("__builtin__", "__main__"):
from ij.io import Opener
opener = Opener()
roi_path = r"R:\Igor BP\Projects\Let-805\Raw Data\Microscopies\Yokogawa Spinning Disk\let-805(syb381)\L4\63x OIL\let-805 localization data\Reanalysis\rois\C2-1.tif_0.roi"
imp = imageloader(r"R:\\Igor BP\\Projects\\Let-805\\Raw Data\\Microscopies\\Yokogawa Spinning Disk\\let-805(syb381)\\L4\\63x OIL\\zprojections\\Stiched\\1.tif")
roi = opener.openRoi(roi_path)
ch = 1
rois = [roi]
output = r"C:\Users\uqibonac\Desktop\test"
th_method = "Li"
analysis_ch = 2
stroke_width = 5
print("Running ...")
print(profile_from_threshold(imp, analysis_ch, rois, stroke_width, th_method, output))
print("Run finished...")