biomedisa 2024.5.14__py3-none-any.whl

biomedisa/biomedisa_features/create_slices.py

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+#!/usr/bin/python3
+##########################################################################
+##                                                                      ##
+##  Copyright (c) 2024 Philipp Lösel. All rights reserved.              ##
+##                                                                      ##
+##  This file is part of the open source project biomedisa.             ##
+##                                                                      ##
+##  Licensed under the European Union Public Licence (EUPL)             ##
+##  v1.2, or - as soon as they will be approved by the                  ##
+##  European Commission - subsequent versions of the EUPL;              ##
+##                                                                      ##
+##  You may redistribute it and/or modify it under the terms            ##
+##  of the EUPL v1.2. You may not use this work except in               ##
+##  compliance with this Licence.                                       ##
+##                                                                      ##
+##  You can obtain a copy of the Licence at:                            ##
+##                                                                      ##
+##  https://joinup.ec.europa.eu/page/eupl-text-11-12                    ##
+##                                                                      ##
+##  Unless required by applicable law or agreed to in                   ##
+##  writing, software distributed under the Licence is                  ##
+##  distributed on an "AS IS" basis, WITHOUT WARRANTIES                 ##
+##  OR CONDITIONS OF ANY KIND, either express or implied.               ##
+##                                                                      ##
+##  See the Licence for the specific language governing                 ##
+##  permissions and limitations under the Licence.                      ##
+##                                                                      ##
+##########################################################################
+
+import sys, os
+BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+sys.path.append(BASE_DIR)
+from biomedisa_features.biomedisa_helper import load_data, color_to_gray, img_to_uint8, img_resize, id_generator
+from PIL import Image
+import numpy as np
+from glob import glob
+import numba
+import shutil
+import cv2
+import tarfile
+
+def unique(arr):
+    arr = arr.astype(np.uint8)
+    counts = np.zeros(256, dtype=int)
+    zsh, ysh, xsh = arr.shape
+    @numba.jit(nopython=True)
+    def __unique__(arr, zsh, ysh, xsh, counts):
+        for k in range(zsh):
+            for l in range(ysh):
+                for m in range(xsh):
+                    index = arr[k,l,m]
+                    counts[index] += 1
+        return counts
+    counts = __unique__(arr, zsh, ysh, xsh, counts)
+    labels = np.where(counts)[0]
+    counts = counts[labels]
+    return labels, counts
+
+def percentile(a, limit):
+    values, counts = unique(a)
+    total_positive = np.sum(counts[1:])
+    limit = total_positive / 100.0 * limit
+    k, tmp = 1, 0
+    while tmp < limit:
+        tmp += counts[k]
+        k += 1
+    low = values[k-1]
+    limit = total_positive - limit
+    k, tmp = -1, total_positive
+    while tmp > limit:
+        tmp -= counts[k]
+        k -= 1
+    high = values[k+1]
+    return low, high
+
+def contrast(arr):
+    bottom_quantile, top_quantile = percentile(arr, 0.5)
+    arr[arr<bottom_quantile] = bottom_quantile
+    arr[arr>top_quantile] = top_quantile
+    values, counts = unique(arr)
+    mean = np.sum(values * counts) / np.sum(counts)
+    std = np.sqrt(np.sum(counts * (values - mean)**2) / (np.sum(counts) - 1))
+    arr = arr.astype(np.float16)
+    arr = (arr - mean) / std
+    amin = (bottom_quantile - mean) / std
+    arr -= amin
+    arr /= (top_quantile - mean) / std - amin
+    arr *= 255.0
+    arr = arr.astype(np.uint8)
+    return arr
+
+def create_slices(path_to_data, path_to_label, on_site=False):
+
+    try:
+        if on_site:
+            path_to_slices = os.path.dirname(path_to_data) + '/slices.' + os.path.splitext(os.path.basename(path_to_data))[0]
+            if os.path.isdir(path_to_slices):
+                shutil.rmtree(path_to_slices)
+            if path_to_label:
+                path_to_label_slices = os.path.dirname(path_to_label) + '/slices.' + os.path.splitext(os.path.basename(path_to_label))[0]
+                if os.path.isdir(path_to_label_slices):
+                    shutil.rmtree(path_to_label_slices)
+        else:
+            path_to_slices = path_to_data.replace('images', 'sliceviewer', 1)
+            if path_to_label:
+                path_to_label_slices = path_to_label.replace('images', 'sliceviewer', 1)
+
+        if not os.path.isdir(path_to_slices) or (path_to_label and not os.path.isdir(path_to_label_slices)):
+
+            # load data and reduce data size
+            path_to_dir, extension = os.path.splitext(path_to_data)
+            if extension == '.gz':
+                path_to_dir, extension = os.path.splitext(path_to_dir)
+            if extension == '.tar' or os.path.isdir(path_to_data):
+                # extract files
+                if extension == '.tar':
+                    path_to_dir = BASE_DIR + '/tmp/' + id_generator(40)
+                    tar = tarfile.open(path_to_data)
+                    tar.extractall(path=path_to_dir)
+                    tar.close()
+                else:
+                    path_to_dir = path_to_data
+                # load files
+                img_names = []
+                for data_type in ['.tif','.tiff','.am','.hdr','.mhd','.mha','.nrrd','.nii','.nii.gz','.zip','.mrc']:
+                    img_names.extend(glob(path_to_dir+'/**/*'+data_type, recursive=True))
+                img_names = sorted(img_names)
+                raw = None
+                for name in img_names:
+                    arr, _ = load_data(name, 'create_slices')
+                    if arr is not None and raw is None:
+                        zsh, ysh, xsh = arr.shape
+                        scale = float(256) / float(max(zsh, ysh, xsh))
+                        z_scale = int(zsh * scale)
+                        y_scale = int(ysh * scale)
+                        x_scale = int(xsh * scale)
+                        raw = img_resize(arr, z_scale, y_scale, x_scale)
+                    elif arr is not None:
+                        arr = img_resize(arr, z_scale, y_scale, x_scale)
+                        raw = np.append(raw, arr, axis=0)
+                # remove extracted files
+                if extension == '.tar' and os.path.isdir(path_to_dir):
+                    shutil.rmtree(path_to_dir)
+            else:
+                raw, _ = load_data(path_to_data, 'create_slices')
+                zsh, ysh, xsh = raw.shape
+                if min(ysh, xsh) > 400 and not on_site:
+                    scale = float(400) / float(min(ysh, xsh))
+                    ysh = int(ysh * scale)
+                    xsh = int(xsh * scale)
+                    tmp = np.empty((zsh, ysh, xsh), dtype=raw.dtype)
+                    for k in range(zsh):
+                        tmp[k] = cv2.resize(raw[k], (xsh, ysh), interpolation=cv2.INTER_AREA)
+                    raw = tmp
+
+            # increase contrast
+            raw = img_to_uint8(raw)
+            raw = contrast(raw)
+
+            # create slices for slice viewer
+            if not os.path.isdir(path_to_slices):
+
+                # make directory
+                os.makedirs(path_to_slices)
+                os.chmod(path_to_slices, 0o770)
+
+                # save slices
+                for k in range(raw.shape[0]):
+                    im = Image.fromarray(raw[k])
+                    im.save(path_to_slices + f'/{k}.png')
+
+            if path_to_label and not os.path.isdir(path_to_label_slices):
+
+                # load data
+                path_to_dir, extension = os.path.splitext(path_to_label)
+                if extension == '.gz':
+                    path_to_dir, extension = os.path.splitext(path_to_dir)
+                if extension == '.tar' or os.path.isdir(path_to_label):
+                    # extract files
+                    if extension == '.tar':
+                        path_to_dir = BASE_DIR + '/tmp/' + id_generator(40)
+                        tar = tarfile.open(path_to_label)
+                        tar.extractall(path=path_to_dir)
+                        tar.close()
+                    else:
+                        path_to_dir = path_to_label
+                    # load files
+                    img_names = []
+                    for data_type in ['.tif','.tiff','.am','.hdr','.mhd','.mha','.nrrd','.nii','.nii.gz','.zip','.mrc']:
+                        img_names.extend(glob(path_to_dir+'/**/*'+data_type, recursive=True))
+                    img_names = sorted(img_names)
+                    # load and scale label data to corresponding img data
+                    mask = np.zeros((0, y_scale, x_scale), dtype=np.uint8)
+                    for name in img_names:
+                        arr, _ = load_data(name, 'create_slices')
+                        if arr is not None:
+                            arr = color_to_gray(arr)
+                            arr = arr.astype(np.uint8)
+                            arr = img_resize(arr, z_scale, y_scale, x_scale, labels=True)
+                            mask = np.append(mask, arr, axis=0)
+                    # remove extracted files
+                    if extension == '.tar' and os.path.isdir(path_to_dir):
+                        shutil.rmtree(path_to_dir)
+                else:
+                    mask, _ = load_data(path_to_label, 'create_slices')
+                    mask = color_to_gray(mask)
+                    mask = mask.astype(np.uint8)
+                    zsh, ysh, xsh = mask.shape
+                    if min(ysh, xsh) > 400 and not on_site:
+                        scale = float(400) / float(min(ysh, xsh))
+                        ysh = int(ysh * scale)
+                        xsh = int(xsh * scale)
+                        tmp = np.zeros((zsh, ysh, xsh), dtype=mask.dtype)
+                        for k in range(zsh):
+                            if np.any(mask[k]):
+                                tmp[k] = cv2.resize(mask[k], (xsh, ysh), interpolation=cv2.INTER_NEAREST)
+                        mask = tmp
+
+                # create slices for slice viewer
+                if mask.shape==raw.shape:
+
+                    # make directory
+                    os.makedirs(path_to_label_slices)
+                    os.chmod(path_to_label_slices, 0o770)
+
+                    # define colors
+                    Color = [(255,0,0),(255,255,0),(0,0,255),(0,100,0),(0,255,0),(255,165,0),(139,0,0),(255,20,147),(255,105,180),(255,0,0),(139,0,139),(255,0,255),(160,32,240),(184,134,11),(255,185,15),(255,215,0),(0,191,255),(16,78,139),(104,131,139),(255,64,64),(165,42,42),(255,127,36),(139,90,43),(110,139,61),(0,255,127),(255,127,80),(139,10,80),(219,112,147),(178,34,34),(255,48,48),(205,79,57),(160,32,240),(255,100,0)] * 8
+                    labels, _ = unique(mask)
+                    labels = labels[1:]
+                    Color = Color[:len(labels)]
+                    Color = np.array(Color, dtype=np.uint8)
+
+                    # allocate memory
+                    zsh, ysh, xsh = raw.shape
+                    if extension == '.tar' or os.path.isdir(path_to_label):
+                        x_shape = 2*xsh
+                    else:
+                        x_shape = xsh
+                    out = np.empty((ysh, x_shape, 3), dtype=np.uint8)
+                    gradient = np.empty((ysh, xsh), dtype=np.uint8)
+
+                    # save preview slice by slice
+                    for k in range(zsh):
+                        raw_tmp = raw[k]
+                        mask_tmp = mask[k]
+                        out.fill(0)
+
+                        # create output slice
+                        for l in range(3):
+                            out[:,:xsh,l] = raw_tmp
+
+                        if np.any(mask_tmp):
+
+                            # compute gradient
+                            gradient.fill(0)
+                            tmp = np.abs(mask_tmp[:-1] - mask_tmp[1:])
+                            tmp[tmp>0] = 1
+                            gradient[:-1] += tmp
+                            gradient[1:] += tmp
+                            tmp = np.abs(mask_tmp[:,:-1] - mask_tmp[:,1:])
+                            tmp[tmp>0] = 1
+                            gradient[:,:-1] += tmp
+                            gradient[:,1:] += tmp
+
+                            # colorize
+                            for j, label in enumerate(labels):
+                                C = Color[j]
+                                tmp = np.logical_and(gradient>0, mask_tmp==label)
+                                out[:,:xsh][tmp] = C
+                                if extension == '.tar' or os.path.isdir(path_to_label):
+                                    out[:,xsh:][mask_tmp==label] = C
+
+                        # save slice
+                        im = Image.fromarray(out)
+                        im.save(path_to_label_slices + f'/{k}.png')
+
+    except Exception as e:
+        print(e)
+
+if __name__ == "__main__":
+    if len(sys.argv)==2:
+        path_to_labels = None
+    else:
+        path_to_labels = sys.argv[2]
+    create_slices(sys.argv[1], path_to_labels, True)
+