biomedisa 2024.5.17__py3-none-any.whl → 2024.5.19__py3-none-any.whl

{biomedisa-2024.5.17.dist-info → biomedisa-2024.5.19.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biomedisa
-Version: 2024.5.17
+Version: 2024.5.19
 Summary: Segmentation of 3D volumetric image data
 Author: Philipp Lösel
 Author-email: philipp.loesel@anu.edu.au
@@ -55,13 +55,8 @@ Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source applica
 
 #### Python example
 ```python
-# change this line to your biomedisa directory
-path_to_biomedisa = '/home/<user>/git/biomedisa'
-
-import sys
-sys.path.append(path_to_biomedisa)
-from biomedisa_features.biomedisa_helper import load_data, save_data
-from biomedisa_features.biomedisa_interpolation import smart_interpolation
+from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.interpolation import smart_interpolation
 
 # load data
 img, _ = load_data('Downloads/trigonopterus.tif')
@@ -81,11 +76,7 @@ save_data('Downloads/final.trigonopterus.smooth.am', smooth_result, header=heade
 
 #### Command-line based
 ```
-# change to the features directory
-cd git/biomedisa/biomedisa_features/
-
-# start smart interpolation
-python biomedisa_interpolation.py C:\Users\%USERNAME%\Downloads\tumor.tif C:\Users\%USERNAME%\Downloads\labels.tumor.tif
+python -m biomedisa.interpolation C:\Users\%USERNAME%\Downloads\tumor.tif C:\Users\%USERNAME%\Downloads\labels.tumor.tif
 ```
 
 # Deep Learning
@@ -93,14 +84,8 @@ python biomedisa_interpolation.py C:\Users\%USERNAME%\Downloads\tumor.tif C:\Use
 
 #### Python example (training)
 ```python
-# change this line to your biomedisa directory
-path_to_biomedisa = '/home/<user>/git/biomedisa'
-
-# load libraries
-import sys
-sys.path.append(path_to_biomedisa)
-from biomedisa_features.biomedisa_helper import load_data
-from biomedisa_features.biomedisa_deeplearning import deep_learning
+from biomedisa.biomedisa_features.biomedisa_helper import load_data
+from biomedisa.deeplearning import deep_learning
 
 # load image data
 img1, _ = load_data('Head1.am')
@@ -129,27 +114,18 @@ deep_learning(img_data, label_data, train=True, batch_size=12,
 
 #### Command-line based (training)
 ```
-# change to the features directory
-cd git/biomedisa/biomedisa_features/
-
 # start training with a batch size of 12
-python biomedisa_deeplearning.py C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t -bs 12
+python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t -bs 12
 
 # validation (optional)
-python biomedisa_deeplearning.py C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t -vi C:\Users\%USERNAME%\Downloads\val_img -vl C:\Users\%USERNAME%\Downloads\val_labels
+python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t -vi C:\Users\%USERNAME%\Downloads\val_img -vl C:\Users\%USERNAME%\Downloads\val_labels
 ```
 If running into ResourceExhaustedError due to out of memory (OOM), try to use smaller batch size.
 
 #### Python example (prediction)
 ```python
-# change this line to your biomedisa directory
-path_to_biomedisa = '/home/<user>/git/biomedisa'
-
-# load libraries
-import sys
-sys.path.append(path_to_biomedisa)
-from biomedisa_features.biomedisa_helper import load_data, save_data
-from biomedisa_features.biomedisa_deeplearning import deep_learning
+from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.deeplearning import deep_learning
 
 # load data
 img, _ = load_data('Head5.am')
@@ -164,20 +140,14 @@ save_data('final.Head5.am', results['regular'], results['header'])
 
 #### Command-line based (prediction)
 ```
-# change to the features directory
-cd git/biomedisa/biomedisa_features/
-
-# start prediction with a batch size of 6
-python biomedisa_deeplearning.py C:\Users\%USERNAME%\Downloads\testing_axial_crop_pat13.nii.gz C:\Users\%USERNAME%\Downloads\heart.h5 -p -bs 6
+python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\testing_axial_crop_pat13.nii.gz C:\Users\%USERNAME%\Downloads\heart.h5 -p
 ```
 
 # Biomedisa Features
 
 #### Load and save data (such as Amira Mesh, TIFF, NRRD, NIfTI or DICOM)
 ```python
-import sys
-sys.path.append(path_to_biomedisa)  # e.g. '/home/<user>/git/biomedisa'
-from biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
 
 # load data as numpy array
 # for DICOM, PNG files, or similar formats, 'path_to_data' must reference
@@ -190,10 +160,8 @@ save_data(path_to_data, data, header)
 
 #### Create STL mesh from segmentation (label values are saved as attributes)
 ```python
-import os, sys
-sys.path.append(path_to_biomedisa)  # e.g. '/home/<user>/git/biomedisa'
-from biomedisa_features.biomedisa_helper import load_data, save_data
-from biomedisa_features.create_mesh import get_voxel_spacing, save_mesh
+from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.mesh import get_voxel_spacing, save_mesh
 
 # load segmentation
 data, header, extension = load_data(path_to_data, return_extension=True)
@@ -209,7 +177,7 @@ save_mesh(path_to_data, data, x_res, y_res, z_res, poly_reduction=0.9, smoothing
 
 #### Create mesh directly
 ```
-python git/biomedisa/biomedisa_features/create_mesh.py <path_to_data>
+python -m biomedisa.mesh <path_to_data>
 ```
 
 #### Options
@@ -225,9 +193,7 @@ python git/biomedisa/biomedisa_features/create_mesh.py <path_to_data>
 
 #### Resize data
 ```python
-import os, sys
-sys.path.append(path_to_biomedisa)  # e.g. '/home/<user>/git/biomedisa'
-from biomedisa_features.biomedisa_helper import img_resize
+from biomedisa.biomedisa_features.biomedisa_helper import img_resize
 
 # resize image data
 zsh, ysh, xsh = data.shape
@@ -240,7 +206,7 @@ label_data = img_resize(label_data, new_zsh, new_ysh, new_xsh, labels=True)
 
 #### Remove outliers and fill holes
 ```python
-from biomedisa_features.biomedisa_helper import clean, fill
+from biomedisa.biomedisa_features.biomedisa_helper import clean, fill
 
 # delete outliers smaller than 90% of the segment
 label_data = clean(label_data, 0.9)
@@ -251,24 +217,28 @@ label_data = fill(label_data, 0.9)
 
 #### Accuracy assessment
 ```python
-from biomedisa_features.biomedisa_helper import Dice_score, ASSD
+from biomedisa.biomedisa_features.biomedisa_helper import Dice_score, ASSD
 dice = Dice_score(ground_truth, result)
 assd = ASSD(ground_truth, result)
 ```
 
 # Update Biomedisa
-If you have used `git clone`, change to the Biomedisa directory and make a pull request.
+If you installed Biomedisa via Pip
+```
+pip install --upgrade biomedisa
+```
+If you used `git clone`, change to the Biomedisa directory and make a pull request
 ```
 cd git/biomedisa
 git pull
 ```
 
-If you have installed the browser based version of Biomedisa (including MySQL database), you also need to update the database.
+If you installed the browser based version of Biomedisa (including MySQL database), you also need to update the database
 ```
 python manage.py migrate
 ```
 
-If you have installed an [Apache Server](https://github.com/biomedisa/biomedisa/blob/master/README/APACHE_SERVER.md), you need to restart the server.
+If you installed an [Apache Server](https://github.com/biomedisa/biomedisa/blob/master/README/APACHE_SERVER.md), you need to restart the server
 ```
 sudo service apache2 restart
 ```

{biomedisa-2024.5.17.dist-info → biomedisa-2024.5.19.dist-info}/RECORD

@@ -1,6 +1,6 @@
 biomedisa/__init__.py,sha256=BLbuGv-c8I8XMzOOnc07qrcWxq8CUA5NM73S3gkixEI,1690
 biomedisa/__main__.py,sha256=a1--8vhtztWEloHVtbM43FZLCfrFo4BELgdsgtWE8ls,536
-biomedisa/deeplearning.py,sha256=eobgRva1ucb1IKpj7SNxmBOsWdZCPAJ-BNbIKnApNeA,27063
+biomedisa/deeplearning.py,sha256=jh6LivGgWSjIoz_2bm-kfnyq90EMiLZwuh6T8Ldj738,27136
 biomedisa/interpolation.py,sha256=mz5Ieiee2RftqisqNzKcCU7IV1n0LGON4zyhvBwE94s,17335
 biomedisa/mesh.py,sha256=6f5klVPoA3zmF3jxLCOUkCXelLtlroS6tJquRHaMwsQ,15920
 biomedisa/biomedisa_features/DataGenerator.py,sha256=FTktX35_FboSzk4UXG_ZN58xXYJqwjX_7ZJ65bzNuFs,12770
@@ -10,12 +10,12 @@ biomedisa/biomedisa_features/PredictDataGeneratorCrop.py,sha256=JBwFcOZMakNMlL5U
 biomedisa/biomedisa_features/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biomedisa/biomedisa_features/active_contour.py,sha256=PUAfCzHKU-p7xeQoWxmDh0ZFbnInXEsafgeE1k-96d0,18131
 biomedisa/biomedisa_features/assd.py,sha256=cXHAhwJqhwOvzgTodlQb21NvYafWTjBJ7_H_icuBNMU,6537
-biomedisa/biomedisa_features/biomedisa_helper.py,sha256=fY7kHLg5VBLF4f_W-p9tZaeqZn6wCq9OHPImZC41GRU,32401
-biomedisa/biomedisa_features/create_slices.py,sha256=gQJev1-DXvqDchGbnLC1bsCtb1gAnv4D82IgOnCJVt8,13329
-biomedisa/biomedisa_features/crop_helper.py,sha256=Op8x10IltAR_5YMotuVHzF3hSbxiOkAchhJM5L0qutw,23894
+biomedisa/biomedisa_features/biomedisa_helper.py,sha256=OhsjzMUhtGLpeo95zU23_LVSyCKcuMm6rXlzG_QO0hk,32294
+biomedisa/biomedisa_features/create_slices.py,sha256=lPYdA2AgwVUJmW94EKrSjKF_lkf7_ROFRSlnLLTQ1EY,13098
+biomedisa/biomedisa_features/crop_helper.py,sha256=jcvMysMfCbarDzayTkc6rY5Tv3Mx37k00yyzSc4Nphw,24533
 biomedisa/biomedisa_features/curvop_numba.py,sha256=9jc4OvHQ6JDN-DaFhRQMLpBDU85HhqzX_YUVBf3Q3vA,7049
 biomedisa/biomedisa_features/django_env.py,sha256=S-ajQpw5A2aBlTYgn_FiyIr02QH05rInzhBDulb9lNg,8989
-biomedisa/biomedisa_features/keras_helper.py,sha256=J4VZNPgdoQSH5wnCcdkubRhxquNmPOUzEAlSkTZltuw,50343
+biomedisa/biomedisa_features/keras_helper.py,sha256=49LTHH_Jn9fyIe5B9uounQNXA86qPjSsvtKAhuEg8qs,50321
 biomedisa/biomedisa_features/nc_reader.py,sha256=7uwdmz4pLC__xb8hWjZ7Y9jrkNJOyD01kIA1EOP8GV0,7406
 biomedisa/biomedisa_features/pid.py,sha256=HAIq52F-PKwDGRyKE74qsY-bdBTs1s85vcIQTKaMIy8,2528
 biomedisa/biomedisa_features/process_image.py,sha256=yxBC3ACV2umscEycXZtY9Hsi1ATws7omnvXROEDfQfA,11159
@@ -37,8 +37,8 @@ biomedisa/biomedisa_features/random_walk/pyopencl_large.py,sha256=cOBhvxrdKCkbr6
 biomedisa/biomedisa_features/random_walk/pyopencl_small.py,sha256=2XALYNNv9D8Gb1u2lcjR1O4W9UM0Xxjj0r4nr-NiEkk,17068
 biomedisa/biomedisa_features/random_walk/rw_large.py,sha256=FERIsTXmqZprGCTShRR75PesIX5MMVtptk-SqI-4abo,19805
 biomedisa/biomedisa_features/random_walk/rw_small.py,sha256=0YFL0Ovb_400Ikbxv5yOXWskl3vAyfQ_0_Gz5EXzvVQ,14881
-biomedisa-2024.5.17.dist-info/LICENSE,sha256=sehayP6UhydNnmstfL4yFR3genMRdpuUh6uZVWJN1H0,14152
-biomedisa-2024.5.17.dist-info/METADATA,sha256=bK2cYJrYfbZGh63SVp6RuZweIX8OPHEda9gAmmIsM_E,11677
-biomedisa-2024.5.17.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-biomedisa-2024.5.17.dist-info/top_level.txt,sha256=opsf1Eb4vCguPSxev4HHSeiUKCccT_C_RcUCdAYbHWQ,10
-biomedisa-2024.5.17.dist-info/RECORD,,
+biomedisa-2024.5.19.dist-info/LICENSE,sha256=sehayP6UhydNnmstfL4yFR3genMRdpuUh6uZVWJN1H0,14152
+biomedisa-2024.5.19.dist-info/METADATA,sha256=81H289XkDEGCBCcKyRtjUVoohr8kZIY1PIquZr9RM_Q,10696
+biomedisa-2024.5.19.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+biomedisa-2024.5.19.dist-info/top_level.txt,sha256=opsf1Eb4vCguPSxev4HHSeiUKCccT_C_RcUCdAYbHWQ,10
+biomedisa-2024.5.19.dist-info/RECORD,,