biomedisa 2024.5.14__tar.gz → 2024.5.16__tar.gz

{biomedisa-2024.5.14 → biomedisa-2024.5.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biomedisa
-Version: 2024.5.14
+Version: 2024.5.16
 Summary: Segmentation of 3D volumetric image data
 Author: Philipp Lösel
 Author-email: philipp.loesel@anu.edu.au
@@ -10,7 +10,7 @@ Project-URL: GitHub, https://github.com/biomedisa/biomedisa
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: European Union Public Licence 1.2 (EUPL 1.2)
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.10
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 

{biomedisa-2024.5.14 → biomedisa-2024.5.16}/pyproject.toml

@@ -4,13 +4,13 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "biomedisa"
-version = "2024.5.14"
+version = "2024.5.16"
 authors = [
   { name="Philipp Lösel"}, {email="philipp.loesel@anu.edu.au" },
 ]
 description = "Segmentation of 3D volumetric image data"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.8"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: European Union Public Licence 1.2 (EUPL 1.2)",

{biomedisa-2024.5.14 → biomedisa-2024.5.16}/src/biomedisa/biomedisa_features/active_contour.py

@@ -33,7 +33,7 @@ if not BASE_DIR in sys.path:
     sys.path.append(BASE_DIR)
 import biomedisa
 from biomedisa_features.curvop_numba import curvop, evolution
-from biomedisa_features.biomedisa_helper import (load_data, save_data,
+from biomedisa_features.biomedisa_helper import (unique_file_path, load_data, save_data,
     pre_processing, img_to_uint8, silent_remove)
 import numpy as np
 import numba
@@ -198,7 +198,6 @@ def activeContour(data, labelData, alpha=1.0, smooth=1, steps=3,
 
         # save result
         if bm.django_env and not bm.remote:
-            from biomedisa_app.views import unique_file_path
             path_to_acwe = unique_file_path(path_to_acwe)
         if bm.path_to_data:
             save_data(path_to_acwe, final, bm.header, bm.final_image_type, bm.compression)
@@ -288,7 +287,7 @@ def init_active_contour(image_id, friend_id, label_id, simple=False):
     django.setup()
     from biomedisa_app.models import Upload
     from biomedisa_app.config import config
-    from biomedisa_app.views import send_data_to_host, qsub_start, qsub_stop, unique_file_path
+    from biomedisa_app.views import send_data_to_host, qsub_start, qsub_stop
 
     # get objects
     try:

{biomedisa-2024.5.14 → biomedisa-2024.5.16}/src/biomedisa/biomedisa_features/biomedisa_helper.py

@@ -43,6 +43,7 @@ import zipfile
 import numba
 import shutil
 import subprocess
+import re
 import math
 
 def silent_remove(filename):
@@ -51,6 +52,56 @@ def silent_remove(filename):
     except OSError:
         pass
 
+# create a unique filename
+def unique_file_path(path, dir_path=BASE_DIR+'/private_storage/'):
+
+    # get extension
+    username = os.path.basename(os.path.dirname(path))
+    filename = os.path.basename(path)
+    filename, extension = os.path.splitext(filename)
+    if extension == '.gz':
+        filename, extension = os.path.splitext(filename)
+        if extension == '.nii':
+            extension = '.nii.gz'
+        elif extension == '.tar':
+            extension = '.tar.gz'
+
+    # get suffix
+    suffix = re.search("-[0-999]"+extension, path)
+    if suffix:
+        suffix = suffix.group()
+        filename = os.path.basename(path)
+        filename = filename[:-len(suffix)]
+        i = int(suffix[1:-len(extension)]) + 1
+    else:
+        suffix = extension
+        i = 1
+
+    # get finaltype
+    addon = ''
+    for feature in ['.filled','.smooth','.acwe','.cleaned','.8bit','.refined', '.cropped',
+                    '.uncertainty','.smooth.cleaned','.cleaned.filled','.denoised']:
+        if filename[-len(feature):] == feature:
+            addon = feature
+
+    if addon:
+        filename = filename[:-len(addon)]
+
+    # maximum lenght of path
+    pic_path = f'images/{username}/{filename}'
+    limit = 100 - len(addon) - len(suffix)
+    path = dir_path + pic_path[:limit] + addon + suffix
+
+    # check if file already exists
+    file_already_exists = os.path.exists(path)
+    while file_already_exists:
+        limit = 100 - len(addon) - len('-') - len(str(i)) - len(extension)
+        path = dir_path + pic_path[:limit] + addon + '-' + str(i) + extension
+        file_already_exists = os.path.exists(path)
+        i += 1
+
+    return path
+
 def Dice_score(ground_truth, result, average_dice=False):
     if average_dice:
         dice = 0

{biomedisa-2024.5.14 → biomedisa-2024.5.16}/src/biomedisa/biomedisa_features/keras_helper.py

@@ -43,7 +43,7 @@ from tensorflow.keras.callbacks import Callback, ModelCheckpoint, EarlyStopping
 from biomedisa_features.DataGenerator import DataGenerator
 from biomedisa_features.PredictDataGenerator import PredictDataGenerator
 from biomedisa_features.biomedisa_helper import (
-    img_resize, load_data, save_data, set_labels_to_zero, id_generator)
+    img_resize, load_data, save_data, set_labels_to_zero, id_generator, unique_file_path)
 from biomedisa_features.remove_outlier import clean, fill
 from biomedisa_features.active_contour import activeContour
 import matplotlib.pyplot as plt
@@ -1148,7 +1148,6 @@ def predict_semantic_segmentation(bm, img, path_to_model,
                 extension = '.nii.gz'
             bm.path_to_final = os.path.splitext(bm.path_to_final)[0] + extension
             if bm.django_env and not bm.remote and not bm.tmp_dir:
-                from biomedisa_app.views import unique_file_path
                 bm.path_to_final = unique_file_path(bm.path_to_final)
 
     # handle amira header

{biomedisa-2024.5.14 → biomedisa-2024.5.16}/src/biomedisa/biomedisa_features/process_image.py

@@ -32,7 +32,7 @@ BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 if not BASE_DIR in sys.path:
     sys.path.append(BASE_DIR)
 import numpy as np
-from biomedisa_features.biomedisa_helper import (load_data, save_data,
+from biomedisa_features.biomedisa_helper import (load_data, save_data, unique_file_path,
     img_to_uint8, smooth_img_3x3)
 from biomedisa_features.create_slices import create_slices
 from shutil import copytree
@@ -46,7 +46,7 @@ def init_process_image(id, process=None):
     django.setup()
     from biomedisa_app.models import Upload
     from biomedisa_app.config import config
-    from biomedisa_app.views import send_data_to_host, qsub_start, qsub_stop, unique_file_path
+    from biomedisa_app.views import send_data_to_host, qsub_start, qsub_stop
     from redis import Redis
     from rq import Queue
 

{biomedisa-2024.5.14 → biomedisa-2024.5.16}/src/biomedisa/biomedisa_features/random_walk/rw_large.py

@@ -28,7 +28,7 @@
 
 from biomedisa_features.remove_outlier import clean, fill
 from biomedisa_features.active_contour import activeContour
-from biomedisa_features.biomedisa_helper import (_get_device, save_data, _error_,
+from biomedisa_features.biomedisa_helper import (_get_device, save_data, _error_, unique_file_path,
     splitlargedata, read_labeled_slices_allx_large, read_labeled_slices_large, sendToChildLarge,
     Dice_score)
 from mpi4py import MPI
@@ -184,7 +184,6 @@ def _diffusion_child(comm, bm=None):
             final_result = final_result[1:-1, 1:-1, 1:-1]
             results['regular'] = final_result
             if bm.django_env and not bm.remote:
-                from biomedisa_app.views import unique_file_path
                 bm.path_to_final = unique_file_path(bm.path_to_final)
             if bm.path_to_data:
                 save_data(bm.path_to_final, final_result, bm.header, bm.final_image_type, bm.compression)

{biomedisa-2024.5.14 → biomedisa-2024.5.16}/src/biomedisa/biomedisa_features/random_walk/rw_small.py

@@ -28,7 +28,7 @@
 
 from biomedisa_features.remove_outlier import clean, fill
 from biomedisa_features.active_contour import activeContour
-from biomedisa_features.biomedisa_helper import (_get_device, save_data,
+from biomedisa_features.biomedisa_helper import (_get_device, save_data, unique_file_path,
     sendToChild, _split_indices, get_labels, Dice_score)
 from mpi4py import MPI
 import numpy as np
@@ -105,9 +105,6 @@ def _diffusion_child(comm, bm=None):
         xsh_gpu = np.int32(xsh_tmp)
         ysh_gpu = np.int32(ysh_tmp)
 
-        if bm.django_env:
-            from biomedisa_app.views import unique_file_path
-
         # smooth
         if bm.smooth:
             try:

{biomedisa-2024.5.14 → biomedisa-2024.5.16}/src/biomedisa/biomedisa_features/remove_outlier.py

@@ -32,7 +32,8 @@ BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 if not BASE_DIR in sys.path:
     sys.path.append(BASE_DIR)
 import biomedisa
-from biomedisa_features.biomedisa_helper import load_data, save_data, silent_remove
+from biomedisa_features.biomedisa_helper import (load_data, save_data,
+    unique_file_path, silent_remove)
 import numpy as np
 from scipy import ndimage
 import argparse
@@ -179,7 +180,6 @@ def main_helper(path_to_labels, img_id=None, friend_id=None, fill_holes=True,
 
     # unique_file_paths
     if django_env and not remote:
-        from biomedisa_app.views import unique_file_path
         path_to_cleaned = unique_file_path(path_to_cleaned)
         path_to_filled = unique_file_path(path_to_filled)
         path_to_cleaned_filled = unique_file_path(path_to_cleaned_filled)
@@ -266,7 +266,7 @@ def init_remove_outlier(image_id, final_id, label_id, fill_holes=True):
     django.setup()
     from biomedisa_app.models import Upload
     from biomedisa_app.config import config
-    from biomedisa_app.views import send_data_to_host, qsub_start, qsub_stop, unique_file_path
+    from biomedisa_app.views import send_data_to_host, qsub_start, qsub_stop
 
     # get objects
     try:

{biomedisa-2024.5.14 → biomedisa-2024.5.16}/src/biomedisa/deeplearning.py

@@ -33,7 +33,7 @@ sys.path.append(BASE_DIR)
 import biomedisa
 import biomedisa_features.crop_helper as ch
 from biomedisa_features.keras_helper import *
-from biomedisa_features.biomedisa_helper import _error_
+from biomedisa_features.biomedisa_helper import _error_, unique_file_path
 from tensorflow.python.framework.errors_impl import ResourceExhaustedError
 import tensorflow as tf
 import numpy as np
@@ -100,8 +100,6 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
 
     # django environment
     if bm.django_env:
-        from biomedisa_app.views import unique_file_path
-        from biomedisa_features.django_env import create_pid_object
 
         # path to image data
         if bm.train:
@@ -130,6 +128,7 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
             project = os.path.splitext(os.path.basename(bm.path_to_model))[0]
 
         # create pid object
+        from biomedisa_features.django_env import create_pid_object
         create_pid_object(os.getpid(), bm.remote, bm.queue, bm.img_id, (bm.path_to_model if bm.train else ''))
 
         # write in log file

{biomedisa-2024.5.14 → biomedisa-2024.5.16}/src/biomedisa/mesh.py

@@ -32,7 +32,7 @@ BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 if not BASE_DIR in sys.path:
     sys.path.append(BASE_DIR)
 import numpy as np
-from biomedisa_features.biomedisa_helper import load_data
+from biomedisa_features.biomedisa_helper import load_data, unique_file_path
 from biomedisa_features.django_env import create_pid_object
 from vtk.util.numpy_support import vtk_to_numpy, numpy_to_vtk
 from stl import mesh
@@ -215,7 +215,7 @@ def init_create_mesh(id):
     django.setup()
     from biomedisa_app.models import Upload
     from biomedisa_app.config import config
-    from biomedisa_app.views import send_data_to_host, qsub_start, qsub_stop, unique_file_path
+    from biomedisa_app.views import send_data_to_host, qsub_start, qsub_stop
 
     # get object
     try:

{biomedisa-2024.5.14 → biomedisa-2024.5.16}/src/biomedisa.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biomedisa
-Version: 2024.5.14
+Version: 2024.5.16
 Summary: Segmentation of 3D volumetric image data
 Author: Philipp Lösel
 Author-email: philipp.loesel@anu.edu.au
@@ -10,7 +10,7 @@ Project-URL: GitHub, https://github.com/biomedisa/biomedisa
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: European Union Public Licence 1.2 (EUPL 1.2)
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.10
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE