diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 3d169ac4074d7951e6a63582eda9bb7332428a80..0319dd474d4ebc23cd4a50bbb4c673a0a1ce678a 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -12,13 +12,11 @@
# trackmate imports
from fiji.plugin.trackmate import Settings
from fiji.plugin.trackmate import TrackMate
-from fiji.plugin.trackmate.cellpose import CellposeDetectorFactory
-from fiji.plugin.trackmate.cellpose.CellposeSettings import PretrainedModel
from fiji.plugin.trackmate.detection import DogDetectorFactory
from fiji.plugin.trackmate.action import LabelImgExporter
# ij imports
from ij import IJ
-from ij.plugin import ZProjector, ImageCalculator
+from ij.plugin import ImageCalculator
from ij.plugin.frame import RoiManager
from ij.measure import ResultsTable
# Bio-Formats imports
@@ -28,8 +26,6 @@ from loci.plugins.in import ImporterOptions
from loci.formats import ImageReader, MetadataTools, Memoizer
# MorpholibJ imports
from inra.ijpb.binary import BinaryImages
-# CLIJ imports
-from net.haesleinhuepf.clij2 import CLIJ2
# imglib2 imports
from net.imglib2.img.display.imagej import ImageJFunctions
from net.imglib2.roi import Regions
@@ -61,114 +57,6 @@ def get_parentdir_filename_ext_from_path(path):
return (parent_dir, filename, ext)
-def tile_image(image_width, image_height, tile_width, tile_height, overlap):
- """ Calculate tiles of an image of given its dimensions. Calculates tile start coordinates and tile dimensions including overlap,
- which can directly be used in Bio-Formats "crop" function. Also calculates tile crop start coordinates and dimensions
- to remove the overlap and the crops start coordinates to re-assemble the original size image. Useful to e.g. segment a large
- already stitched image tile by tile.
-
- Parameters
- ----------
- image_width : int
- the input images width in pixels
- image_height : int
- the input images height in pixels
- tile_width : int
- the desired tile width in pixels
- tile_height : int
- the desired tile height in pixels
- overlap : int
- the desired tile overlap in pixels
-
- Returns
- -------
- list
- all_tile_regions: tile coordinates and dimensions including overlap
- all_crop_regions: tile coordinates and dimensions to remove the overlap again
- all_tile_start_no_overlap: start coordinates of the tiles without overlap to re-assemble the original size image
- """
- # TODO: this function likely needs refactoring to be more clear and readable
- number_of_columns = image_width // tile_width # is a floored division
- column_remainder_px = image_width % tile_width
- number_of_rows = image_height // tile_height
- row_remainder_px = image_height % tile_height
- all_tile_regions = []
- all_crop_regions = []
- all_tile_start_no_overlap = []
-
- for current_row in range(number_of_rows):
- if current_row == number_of_rows -1 :
- tile_height_boarder_addition = row_remainder_px # increase tile height in the last row
- else:
- tile_height_boarder_addition = 0
-
- for current_column in range (number_of_columns):
- if current_column == number_of_columns - 1 :
- tile_width_boarder_addition = column_remainder_px # increase tile width in the last column
- else:
- tile_width_boarder_addition = 0
-
- tile_start_x_no_overlap = current_column * tile_width
- tile_start_y_no_overlap = current_row * tile_height
-
- if current_column > 0:
- tile_start_x = current_column * tile_width - overlap
- crop_start_x = overlap
- else:
- tile_start_x = 0
- crop_start_x = 0
-
- if current_row > 0:
- tile_start_y = current_row * tile_height - overlap
- crop_start_y = overlap
- else:
- tile_start_y = 0
- crop_start_y = 0
-
- if current_column == 0 or current_column == number_of_columns - 1:
- current_tile_width = tile_width + overlap + tile_width_boarder_addition
- else:
- current_tile_width = tile_width + 2 * overlap
-
- if current_row == 0 or current_row == number_of_rows - 1:
- current_tile_height = tile_height + overlap + tile_height_boarder_addition
- else:
- current_tile_height = tile_height + 2 * overlap
-
- tile_region = [tile_start_x, tile_start_y, current_tile_width, current_tile_height]
- crop_region = [crop_start_x, crop_start_y, current_tile_width - overlap, current_tile_height - overlap]
- tile_start_no_overlap = [tile_start_x_no_overlap, tile_start_y_no_overlap]
-
- all_tile_regions.append(tile_region)
- all_crop_regions.append(crop_region)
- all_tile_start_no_overlap.append(tile_start_no_overlap)
-
- return all_tile_regions, all_crop_regions, all_tile_start_no_overlap
-
-
-def create_empty_image(bit_depth, image_width, image_height):
- """creates an empty image of given dimensions. The image is 2D, filled with black pixels of value 0.
-
- Parameters
- ----------
- bit_depth : int
- the image bit dept
- image_width : int
- image width in px
- image_height : int
- image height in px
-
- Returns
- -------
- ImagePlus
- the empty image
- """
-
- canvas = IJ.createImage("mosaic", str(bit_depth) + "-bit black", image_width, image_height, 1)
-
- return canvas
-
-
def write_bf_memoryfile(path_to_file):
"""Write a BF memo-file so subsequent access to the same file is faster.
@@ -321,53 +209,6 @@ def run_trackmate_dog_spot_detector(imp, spot_diameter, quality_threshold):
return label_imp
-def run_trackmate_cellpose_detector(imp):
- """Run TrackMates CellPose detector on a target image
-
- Parameters
- ----------
- imp : ImagePlus
- the input image
-
- Returns
- -------
- ImagePlus
- a label image of the detected regions.
- """
-
- cal = imp.getCalibration()
- settings = Settings(imp)
-
- # TODO: expose more parameters
- settings.detectorFactory = CellposeDetectorFactory()
- settings.detectorSettings['TARGET_CHANNEL'] = 0
- settings.detectorSettings['OPTIONAL_CHANNEL_2'] = 0
- settings.detectorSettings['CELLPOSE_PYTHON_FILEPATH'] = 'S:/cellpose_env/python.exe'
- settings.detectorSettings['CELLPOSE_MODEL_FILEPATH'] = ''
- settings.detectorSettings['CELLPOSE_MODEL'] = PretrainedModel.CYTO
- settings.detectorSettings['CELL_DIAMETER'] = 30.0
- settings.detectorSettings['USE_GPU'] = True
- settings.detectorSettings['SIMPLIFY_CONTOURS'] = True
-
- trackmate = TrackMate(settings)
- trackmate.computeSpotFeatures(False)
- trackmate.computeTrackFeatures(False)
-
- if not trackmate.checkInput():
- print( str( trackmate.getErrorMessage() ) )
-
- if not trackmate.process():
- print( str( trackmate.getErrorMessage() ) )
-
- exportSpotsAsDots = False
- exportTracksOnly = False
- label_imp = LabelImgExporter.createLabelImagePlus(trackmate, exportSpotsAsDots, exportTracksOnly, False)
- label_imp.setCalibration(cal)
- imp.close()
-
- return label_imp
-
-
def get_threshold_from_method(imp, method):
"""returns the threshold value of chosen IJ AutoThreshold method from a stack (hyperstack?)
@@ -423,109 +264,6 @@ def convert_to_binary(imp, threshold=1, scale_binary=True):
return mask_imp
-def erode_labelimp_gpu(label_imp, radius, relabel_islands=True):
- """Erode a label image on the GPU.
-
- Parameters
- ----------
- label_imp : ImagePlus
- the input image
- radius : float
- radius used for erosion
- relabel_islands : bool, optional
- if True, split objects will get new labels each , by default True
-
- Returns
- -------
- ImagePlus
- the eroded label image
- """
-
- clij2 = CLIJ2.getInstance()
- labels_input = clij2.push(label_imp)
- labels_destination = clij2.create(labels_input)
- radius = 1.0
- clij2.erodeLabels(labels_input, labels_destination, radius, relabel_islands)
- eroded_labelimp = clij2.pull(labels_destination)
- clij2.release(labels_input)
- clij2.release(labels_destination)
- label_imp.close()
-
- return eroded_labelimp
-
-
-def remove_tileoverlap(imp, crop_region):
- """Crop an image to specified dimensions.
- The operation is destructive, the original image is lost.
-
- Parameters
- ----------
- imp : ImagePlus
- the input image
- crop_region : list or array of int
- the crop region in the format of [start_x, start_y, crop_width, crop_height]
-
- Returns
- -------
- ImagePlus
- the cropped image
- """
-
- start_x = crop_region[0]
- start_y = crop_region[1]
- crop_width = crop_region[2]
- crop_height = crop_region[3]
- imp.setRoi(start_x, start_y, crop_width, crop_height)
- cropped_imp = imp.crop()
- imp.close()
-
- return cropped_imp
-
-
-def copy_and_paste_image(source, target, start_coordinates_xy):
- """Copy the source image and paste it into the target image
-
- Parameters
- ----------
- source : ImagePlus
- the source image
- target : ImagePlus
- the target image
- start_coordinates_xy : list or array of int
- the x and y coordinates in the target image where the source image will be pasted
- """
- source.copy()
- start_x = start_coordinates_xy[0]
- start_y = start_coordinates_xy[1]
- target.paste(start_x, start_y)
- source.close()
-
-
-def merge_touching_labels(label_imp, bit_depth):
- """merge touching labels in a label image so they have the same label ID.
-
- Parameters
- ----------
- label_imp : ImagePlus
- the label image with touching labels of different label ID
- bit_depth : int
- the image bit depth
-
- Returns
- -------
- ImagePlus
- the label image with merged touching labels
- """
-
- binary_imp = BinaryImages.binarize(label_imp)
- connectivity = 8
- merged_label_imp = BinaryImages.componentsLabeling(binary_imp, connectivity, bit_depth)
- label_imp.close()
- binary_imp.close()
-
- return merged_label_imp
-
-
def save_image_as_IJtif(imp, filename, suffix, target):
"""Save the image as ImageJ-Tiff
@@ -547,25 +285,6 @@ def save_image_as_IJtif(imp, filename, suffix, target):
IJ.saveAs(imp, "Tiff", savepath)
-def measure_label_size_shape_2d(label_imp):
- rm = RoiManager.getInstance()
- if not rm:
- rm = RoiManager()
- rm.reset()
- rt = ResultsTable()
-
- command.run( Labels2Rois , False , 'imp' , label_imp , 'rm', rm).get()
- IJ.run("Set Measurements...", "area centroid perimeter shape feret's redirect=None decimal=3")
- rm.runCommand(label_imp,"Deselect")
- rm.runCommand(label_imp,"Measure")
- rm.reset()
- IJ.renameResults("Results", "Size and shape features")
- results_table = rt.getResultsTable("Size and shape features")
-
-
- return results_table
-
-
def convert_labelimage_to_imglib2regions(imp):
"""Convert a ImagePlus label image to imglib2 regions