biomedisa 2024.5.14__py3-none-any.whl

biomedisa/biomedisa_features/curvop_numba.py

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+##########################################################################
+##                                                                      ##
+##  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 numpy as np
+import numba
+
+@numba.jit(nopython=True)
+def evolution(mean, A, data, alpha):
+    zsh, ysh, xsh = A.shape
+    B = np.copy(A)
+    for k in range(1, zsh-1):
+        for l in range(1, ysh-1):
+            for m in range(1, xsh-1):
+                refLabel = A[k,l,m]
+                finLabel = refLabel
+                img = data[k,l,m]
+                if refLabel == 0:
+                    ref = alpha * abs(mean[refLabel] - img)
+                else:
+                    ref = abs(mean[refLabel] - img)
+                for n in range(-1, 2):
+                    for o in range(-1, 2):
+                        for p in range(-1, 2):
+                            tmpLabel = A[k+n, l+o, m+p]
+                            if tmpLabel != refLabel:
+                                if tmpLabel == 0:
+                                    val = alpha * abs(mean[tmpLabel] - img)
+                                else:
+                                    val = abs(mean[tmpLabel] - img)
+                                if val < ref:
+                                    ref = val
+                                    finLabel = tmpLabel
+                B[k,l,m] = finLabel
+    return B
+
+@numba.jit(nopython=True)
+def erosion(start, final, _P3, zsh, ysh, xsh, label):
+    for plane in range(1, zsh-1):
+        for row in range(1, ysh-1):
+            for column in range(1, xsh-1):
+                found = 0
+                for n in range(-1, 2):
+                    for o in range(-1, 2):
+                        for p in range(-1, 2):
+                            if start[plane+n, row+o, column+p] != label:
+                                found = 1
+                if start[plane, row, column] == label and found == 1:
+                    t, found = 0, 0
+                    while t < 9 and found == 0:
+                        value = 0
+                        for k in range(3):
+                            for l in range(3):
+                                for m in range(3):
+                                    if _P3[t,k,l,m] == 1:
+                                        value += abs(start[plane-1+k, row-1+l, column-1+m] - label)
+                        if value == 0:
+                            found = 1
+                        t += 1
+                    if found == 0:
+                        subLabel = label
+                        for n in range(-1, 2):
+                            for o in range(-1, 2):
+                                for p in range(-1, 2):
+                                    tmpLabel = start[plane+n, row+o, column+p]
+                                    if tmpLabel != label:
+                                        subLabel = tmpLabel
+                        final[plane, row, column] = subLabel
+    return start, final
+
+@numba.jit(nopython=True)
+def dilation(start, final, _P3, zsh, ysh, xsh, label):
+    for plane in range(1, zsh-1):
+        for row in range(1, ysh-1):
+            for column in range(1, xsh-1):
+                found = 0
+                for n in range(-1, 2):
+                    for o in range(-1, 2):
+                        for p in range(-1, 2):
+                            if start[plane+n, row+o, column+p] == label:
+                                found = 1
+                if start[plane, row, column] != label and found == 1:
+                    t, found = 0, 0
+                    while t < 9 and found == 0:
+                        value = 0
+                        for k in range(3):
+                            for l in range(3):
+                                for m in range(3):
+                                    if _P3[t,k,l,m] == 1 and start[plane-1+k, row-1+l, column-1+m] != label:
+                                        value += 0
+                                    else:
+                                        value += 1
+                        if value == 0:
+                            found = 1
+                        t += 1
+                    if found == 0:
+                        final[plane, row, column] = label
+    return start, final
+
+def curvop(start, steps, label, allLabels):
+    zsh, ysh, xsh = start.shape
+    final = np.copy(start, order='C')
+    _P3 = np.zeros((9,3,3,3), dtype=np.int32)
+    _P3[0,:,:,1] = 1
+    _P3[1,:,1,:] = 1
+    _P3[2,1,:,:] = 1
+    _P3[3,:,[0,1,2],[0,1,2]] = 1
+    _P3[4,:,[0,1,2],[2,1,0]] = 1
+    _P3[5,[0,1,2],:,[0,1,2]] = 1
+    _P3[6,[0,1,2],:,[2,1,0]] = 1
+    _P3[7,[0,1,2],[0,1,2],:] = 1
+    _P3[8,[0,1,2],[2,1,0],:] = 1
+    for k in range(steps):
+        if k % 2 == 0:
+            start, final = erosion(start, final, _P3, zsh, ysh, xsh, label)
+            start = np.copy(final, order='C')
+            final, start = dilation(final, start, _P3, zsh, ysh, xsh, label)
+            final = np.copy(start, order='C')
+        else:
+            start, final = dilation(start, final, _P3, zsh, ysh, xsh, label)
+            start = np.copy(final, order='C')
+            final, start = erosion(final, start, _P3, zsh, ysh, xsh, label)
+            final = np.copy(start, order='C')
+    return start
+

biomedisa/biomedisa_features/django_env.py

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+##########################################################################
+##                                                                      ##
+##  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__)))
+import subprocess
+
+def create_error_object(message, remote=False, queue=None, img_id=None):
+
+    # remote server
+    if remote:
+        with open(BASE_DIR + f'/log/error_{queue}', 'w') as errorfile:
+            print(message, file=errorfile)
+
+    # local server
+    else:
+        import django
+        django.setup()
+        from biomedisa_app.models import Upload
+        from biomedisa_app.views import send_error_message
+        image = Upload.objects.get(pk=img_id)
+        Upload.objects.create(user=image.user, project=image.project, log=1, imageType=None, shortfilename=message)
+        send_error_message(image.user.username, image.shortfilename, message)
+
+        # stop processing
+        image.path_to_model = ''
+        image.status = 0
+        image.pid = 0
+        image.save()
+
+def create_pid_object(pid, remote=False, queue=None, img_id=None, path_to_model=''):
+
+    # remote server
+    if remote:
+        with open(BASE_DIR + f'/log/pid_{queue}', 'w') as pidfile:
+            print(pid, file=pidfile)
+
+    # local server
+    else:
+        import django
+        django.setup()
+        from biomedisa_app.models import Upload
+        image = Upload.objects.get(pk=img_id)
+        image.path_to_model = path_to_model
+        image.pid = pid
+        image.save()
+
+def post_processing(path_to_final, time_str, server_name, remote, queue, dice=1.0, path_to_model=None, path_to_uq=None, path_to_smooth=None, path_to_cropped_image=None, uncertainty=False, smooth=False, img_id=None, label_id=None, train=False, predict=False, validation=False):
+
+    # remote server
+    if remote:
+        with open(BASE_DIR + f'/log/config_{queue}', 'w') as configfile:
+            print(path_to_final, path_to_uq, path_to_smooth, uncertainty, smooth, str(time_str).replace(' ','-'), server_name, path_to_model, path_to_cropped_image, dice, file=configfile)
+
+    # local server
+    else:
+        import django
+        django.setup()
+        from biomedisa_app.models import Upload
+        from biomedisa_app.views import send_notification
+        from biomedisa_features.active_contour import init_active_contour
+        from biomedisa_features.remove_outlier import init_remove_outlier
+        from biomedisa_features.create_slices import create_slices
+        from redis import Redis
+        from rq import Queue
+
+        # get object
+        image = Upload.objects.get(pk=img_id)
+
+        if train:
+            # create model object
+            shortfilename = os.path.basename(path_to_model)
+            filename = 'images/' + image.user.username + '/' + shortfilename
+            Upload.objects.create(pic=filename, user=image.user, project=image.project, imageType=4, shortfilename=shortfilename)
+
+            if validation:
+                # create acc object
+                shortfilename = os.path.basename(path_to_model.replace('.h5','_acc.png'))
+                filename = 'images/' + image.user.username + '/' + shortfilename
+                Upload.objects.create(pic=filename, user=image.user, project=image.project, imageType=6, shortfilename=shortfilename)
+
+                # create loss object
+                shortfilename = os.path.basename(path_to_model.replace('.h5','_loss.png'))
+                filename = 'images/' + image.user.username + '/' + shortfilename
+                Upload.objects.create(pic=filename, user=image.user, project=image.project, imageType=6, shortfilename=shortfilename)
+
+        else:
+            # create final objects
+            shortfilename = os.path.basename(path_to_final)
+            filename = 'images/' + image.user.username + '/' + shortfilename
+            final = Upload.objects.create(pic=filename, user=image.user, project=image.project, final=1, active=1, imageType=3, shortfilename=shortfilename)
+            final.friend = final.id
+            final.save()
+
+            if path_to_cropped_image:
+                shortfilename = os.path.basename(path_to_cropped_image)
+                filename = 'images/' + image.user.username + '/' + shortfilename
+                Upload.objects.create(pic=filename, user=image.user, project=image.project, final=9, active=0, imageType=3, shortfilename=shortfilename, friend=final.id)
+
+            if uncertainty:
+                shortfilename = os.path.basename(path_to_uq)
+                filename = 'images/' + image.user.username + '/' + shortfilename
+                uncertainty_obj = Upload.objects.create(pic=filename, user=image.user, project=image.project, final=4, imageType=3, shortfilename=shortfilename, friend=final.id)
+
+            if smooth:
+                shortfilename = os.path.basename(path_to_smooth)
+                filename = 'images/' + image.user.username + '/' + shortfilename
+                smooth_obj = Upload.objects.create(pic=filename, user=image.user, project=image.project, final=5, imageType=3, shortfilename=shortfilename, friend=final.id)
+
+            # create allaxes warning
+            if dice < 0.3:
+                Upload.objects.create(user=image.user, project=image.project,
+                    log=1, imageType=None, shortfilename='Bad result! Activate "All axes" if you labeled axes other than the xy-plane.')
+
+            # acwe
+            if not (os.path.splitext(path_to_final)[1]=='.tar' or path_to_final[-7:]=='.tar.gz'):
+                q = Queue('acwe', connection=Redis())
+                job = q.enqueue_call(init_active_contour, args=(img_id, final.id, label_id, True,), timeout=-1)
+                job = q.enqueue_call(init_active_contour, args=(img_id, final.id, label_id,), timeout=-1)
+
+            # cleanup
+            if not (os.path.splitext(path_to_final)[1]=='.tar' or path_to_final[-7:]=='.tar.gz'):
+                q = Queue('cleanup', connection=Redis())
+                job = q.enqueue_call(init_remove_outlier, args=(img_id, final.id, label_id,), timeout=-1)
+                if smooth:
+                    job = q.enqueue_call(init_remove_outlier, args=(img_id, smooth_obj.id, label_id, False,), timeout=-1)
+
+            # create slices
+            q = Queue('slices', connection=Redis())
+            job = q.enqueue_call(create_slices, args=(image.pic.path, final.pic.path,), timeout=-1)
+            if path_to_cropped_image:
+                q = Queue('slices', connection=Redis())
+                job = q.enqueue_call(create_slices, args=(path_to_cropped_image, None,), timeout=-1)
+            if smooth:
+                job = q.enqueue_call(create_slices, args=(image.pic.path, smooth_obj.pic.path,), timeout=-1)
+            if uncertainty:
+                job = q.enqueue_call(create_slices, args=(uncertainty_obj.pic.path, None,), timeout=-1)
+
+        # send notification
+        send_notification(image.user.username, image.shortfilename, time_str, server_name, train, predict)
+
+        # stop processing
+        image.path_to_model = ''
+        image.status = 0
+        image.pid = 0
+        image.save()
+