biomedisa 2024.5.21__py3-none-any.whl → 2024.5.22__py3-none-any.whl

biomedisa/deeplearning.py

@@ -42,6 +42,7 @@ import time
 import subprocess
 import glob
 import tempfile
+import tifffile
 
 class Biomedisa(object):
      pass
@@ -55,6 +56,11 @@ def get_gpu_memory():
     except:
         return None
 
+def number_of_slices(file_path):
+    with tifffile.TiffFile(file_path) as tiff:
+        z_dim = len(tiff.pages)
+    return z_dim
+
 def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=None,
     path_to_images=None, path_to_labels=None, val_images=None, val_labels=None,
     path_to_model=None, predict=False, train=False, header_file=None,
@@ -248,8 +254,16 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
             # list of images
             path_to_finals = []
             if bm.path_to_images is not None and os.path.isdir(bm.path_to_images):
-                files = glob.glob(bm.path_to_images+'/**/*', recursive=True)
-                bm.path_to_images = [f for f in files if os.path.isfile(f)]
+                # load list of volumetric image files
+                files = []
+                for data_type in ['.am','.hdr','.mhd','.mha','.nrrd','.nii','.nii.gz','.zip','.mrc']:
+                    files += [file for file in glob.glob(bm.path_to_images+'/**/*'+data_type, recursive=True) if not os.path.basename(file).startswith('.')]
+                for data_type in ['.tif','.tiff']:
+                    files += [file for file in glob.glob(bm.path_to_images+'/**/*'+data_type, recursive=True) if not os.path.basename(file).startswith('.') and number_of_slices(file)>1]
+                if len(files)==0: # assume directory of 2D slices
+                    bm.path_to_images = [bm.path_to_images]
+                else:
+                    bm.path_to_images = files
             else:
                 bm.path_to_images = [bm.path_to_images]
 

{biomedisa-2024.5.21.dist-info → biomedisa-2024.5.22.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biomedisa
-Version: 2024.5.21
+Version: 2024.5.22
 Summary: Segmentation of 3D volumetric image data
 Author: Philipp Lösel
 Author-email: philipp.loesel@anu.edu.au
@@ -50,11 +50,18 @@ Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source applica
 + Download the data from our [gallery](https://biomedisa.info/gallery/)
 
 ## Revisions
-2024.05.21
+2024.05.22
 + Pip is the preferred installation method
 + Commands, module names and imports have been changed to conform to the Pip standard
 + For versions <=2023.09.1 please check [README](https://github.com/biomedisa/biomedisa/blob/master/README/deprecated/README_2023.09.1.md)
 
+## Quickstart
+Install the Biomedisa package from the [Python Package Index](https://pypi.org/project/biomedisa/):
+```
+python -m pip install -U biomedisa
+```
+For smart interpolation and deep Learning modules, follow the [installation instructions](https://github.com/biomedisa/biomedisa#installation-command-line-based).
+
 ## Smart Interpolation
 + [Parameters and Examples](https://github.com/biomedisa/biomedisa/blob/master/README/smart_interpolation.md)
 

{biomedisa-2024.5.21.dist-info → biomedisa-2024.5.22.dist-info}/RECORD

@@ -1,6 +1,6 @@
 biomedisa/__init__.py,sha256=hw4mzEjGFXm-vxus2DBfKFW0nKoG0ibL5SH6ShfchrY,1526
 biomedisa/__main__.py,sha256=a1--8vhtztWEloHVtbM43FZLCfrFo4BELgdsgtWE8ls,536
-biomedisa/deeplearning.py,sha256=dVwLkijm0ibtn6zUUV3t2WK6Fzvks4VlgzKNLqzDpAQ,27064
+biomedisa/deeplearning.py,sha256=UG5baX58CrO8YXe9pU6_Bp2OOvbC74LQw4S33HqM2iA,27828
 biomedisa/interpolation.py,sha256=R8UbBWt7vOuiQCPSeNIpEY0_yfQUg1oBfhAjXi91Hl4,17253
 biomedisa/mesh.py,sha256=glvpTN0PPByb5j2IbLCdWQtc5O4VT-Pwu3en8EaYyTo,15819
 biomedisa/features/DataGenerator.py,sha256=bGys6UZ0bnKb_k1Y3Spo6MNPk_goSAmptdZnI39smaw,12770
@@ -37,8 +37,8 @@ biomedisa/features/random_walk/pyopencl_large.py,sha256=q79AxG3p3qFjxfiAZfUK9I5B
 biomedisa/features/random_walk/pyopencl_small.py,sha256=opNlS-qzOa9qWafBNJdvf6r1aRAFf7_JXf6ISDnkdXE,17068
 biomedisa/features/random_walk/rw_large.py,sha256=ZnITvk00Y11ZZlGuBRaJO1EwU0wYBdEwdpj9vvXCqF4,19805
 biomedisa/features/random_walk/rw_small.py,sha256=RPzZe24YrEwYelJukDjvqaoD_SyhgdriEi7uV3kZGXI,14881
-biomedisa-2024.5.21.dist-info/LICENSE,sha256=sehayP6UhydNnmstfL4yFR3genMRdpuUh6uZVWJN1H0,14152
-biomedisa-2024.5.21.dist-info/METADATA,sha256=GJ9BXl6MH84zMYZrpShMBkSDZx50dYIKWDE97EWj1-w,10465
-biomedisa-2024.5.21.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-biomedisa-2024.5.21.dist-info/top_level.txt,sha256=opsf1Eb4vCguPSxev4HHSeiUKCccT_C_RcUCdAYbHWQ,10
-biomedisa-2024.5.21.dist-info/RECORD,,
+biomedisa-2024.5.22.dist-info/LICENSE,sha256=sehayP6UhydNnmstfL4yFR3genMRdpuUh6uZVWJN1H0,14152
+biomedisa-2024.5.22.dist-info/METADATA,sha256=jKMlVJyzFHJ37MREWXc9UbUuDoxVA36hYr-1egUfnhY,10786
+biomedisa-2024.5.22.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+biomedisa-2024.5.22.dist-info/top_level.txt,sha256=opsf1Eb4vCguPSxev4HHSeiUKCccT_C_RcUCdAYbHWQ,10
+biomedisa-2024.5.22.dist-info/RECORD,,