biomedisa 2024.5.17__tar.gz → 2024.5.19__tar.gz

{biomedisa-2024.5.17 → biomedisa-2024.5.19}/PKG-INFO

@@ -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 → biomedisa-2024.5.19}/README.md

@@ -39,13 +39,8 @@ 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')
@@ -65,11 +60,7 @@ 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
@@ -77,14 +68,8 @@ 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')
@@ -113,27 +98,18 @@ 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')
@@ -148,20 +124,14 @@ 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
@@ -174,10 +144,8 @@ 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)
@@ -193,7 +161,7 @@ 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
@@ -209,9 +177,7 @@ 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
@@ -224,7 +190,7 @@ 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)
@@ -235,24 +201,28 @@ 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 → biomedisa-2024.5.19}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "biomedisa"
-version = "2024.5.17"
+version = "2024.5.19"
 authors = [
   { name="Philipp Lösel"}, {email="philipp.loesel@anu.edu.au" },
 ]

{biomedisa-2024.5.17 → biomedisa-2024.5.19}/src/biomedisa/biomedisa_features/biomedisa_helper.py

@@ -41,10 +41,10 @@ import cv2
 import time
 import zipfile
 import numba
-import shutil
 import subprocess
 import re
 import math
+import tempfile
 
 def silent_remove(filename):
     try:
@@ -280,92 +280,85 @@ def load_data(path_to_data, process='None', return_extension=False):
             data, header = None, None
 
     elif extension == '.zip' or os.path.isdir(path_to_data):
-        # extract files
-        if extension=='.zip':
-            path_to_dir = BASE_DIR + '/tmp/' + id_generator(40)
-            try:
-                zip_ref = zipfile.ZipFile(path_to_data, 'r')
-                zip_ref.extractall(path=path_to_dir)
-                zip_ref.close()
-            except Exception as e:
-                print(e)
-                print('Using unzip package...')
-                try:
-                    success = subprocess.Popen(['unzip',path_to_data,'-d',path_to_dir]).wait()
-                    if success != 0:
-                        if os.path.isdir(path_to_dir):
-                            shutil.rmtree(path_to_dir)
-                        data, header = None, None
-                except Exception as e:
-                    print(e)
-                    if os.path.isdir(path_to_dir):
-                        shutil.rmtree(path_to_dir)
-                    data, header = None, None
-            path_to_data = path_to_dir
-
-        # load files
-        if os.path.isdir(path_to_data):
-            files = []
-            for data_type in ['.[pP][nN][gG]','.[tT][iI][fF]','.[tT][iI][fF][fF]','.[dD][cC][mM]','.[dD][iI][cC][oO][mM]','.[bB][mM][pP]','.[jJ][pP][gG]','.[jJ][pP][eE][gG]','.nc','.nc.bz2']:
-                files += [file for file in glob.glob(path_to_data+'/**/*'+data_type, recursive=True) if not os.path.basename(file).startswith('.')]
-            nc_extension = False
-            for file in files:
-                if os.path.splitext(file)[1] == '.nc' or os.path.splitext(os.path.splitext(file)[0])[1] == '.nc':
-                    nc_extension = True
-            if nc_extension:
+        with tempfile.TemporaryDirectory() as temp_dir:
+
+            # extract files
+            if extension=='.zip':
                 try:
-                    data, header = nc_to_np(path_to_data)
+                    zip_ref = zipfile.ZipFile(path_to_data, 'r')
+                    zip_ref.extractall(path=temp_dir)
+                    zip_ref.close()
                 except Exception as e:
                     print(e)
-                    data, header = None, None
-            else:
-                try:
-                    # remove unreadable files or directories
-                    for name in files:
-                        if os.path.isfile(name):
-                            try:
-                                img, _ = load(name)
-                            except:
+                    print('Using unzip package...')
+                    try:
+                        success = subprocess.Popen(['unzip',path_to_data,'-d',temp_dir]).wait()
+                        if success != 0:
+                            data, header = None, None
+                    except Exception as e:
+                        print(e)
+                        data, header = None, None
+                path_to_data = temp_dir
+
+            # load files
+            if os.path.isdir(path_to_data):
+                files = []
+                for data_type in ['.[pP][nN][gG]','.[tT][iI][fF]','.[tT][iI][fF][fF]','.[dD][cC][mM]','.[dD][iI][cC][oO][mM]','.[bB][mM][pP]','.[jJ][pP][gG]','.[jJ][pP][eE][gG]','.nc','.nc.bz2']:
+                    files += [file for file in glob.glob(path_to_data+'/**/*'+data_type, recursive=True) if not os.path.basename(file).startswith('.')]
+                nc_extension = False
+                for file in files:
+                    if os.path.splitext(file)[1] == '.nc' or os.path.splitext(os.path.splitext(file)[0])[1] == '.nc':
+                        nc_extension = True
+                if nc_extension:
+                    try:
+                        data, header = nc_to_np(path_to_data)
+                    except Exception as e:
+                        print(e)
+                        data, header = None, None
+                else:
+                    try:
+                        # remove unreadable files or directories
+                        for name in files:
+                            if os.path.isfile(name):
+                                try:
+                                    img, _ = load(name)
+                                except:
+                                    files.remove(name)
+                            else:
                                 files.remove(name)
+                        files.sort()
+
+                        # get data size
+                        img, _ = load(files[0])
+                        if len(img.shape)==3:
+                            ysh, xsh, csh = img.shape[0], img.shape[1], img.shape[2]
+                            channel = 'last'
+                            if ysh < csh:
+                                csh, ysh, xsh = img.shape[0], img.shape[1], img.shape[2]
+                                channel = 'first'
                         else:
-                            files.remove(name)
-                    files.sort()
-
-                    # get data size
-                    img, _ = load(files[0])
-                    if len(img.shape)==3:
-                        ysh, xsh, csh = img.shape[0], img.shape[1], img.shape[2]
-                        channel = 'last'
-                        if ysh < csh:
-                            csh, ysh, xsh = img.shape[0], img.shape[1], img.shape[2]
-                            channel = 'first'
-                    else:
-                        ysh, xsh = img.shape[0], img.shape[1]
-                        csh, channel = 0, None
-
-                    # load data slice by slice
-                    data = np.empty((len(files), ysh, xsh), dtype=img.dtype)
-                    header, image_data_shape = [], []
-                    for k, file_name in enumerate(files):
-                        img, img_header = load(file_name)
-                        if csh==3:
-                            img = rgb2gray(img, channel)
-                        elif csh==1 and channel=='last':
-                            img = img[:,:,0]
-                        elif csh==1 and channel=='first':
-                            img = img[0,:,:]
-                        data[k] = img
-                        header.append(img_header)
-                    header = [header, files, data.dtype]
-                    data = np.swapaxes(data, 1, 2)
-                    data = np.copy(data, order='C')
-                except Exception as e:
-                    print(e)
-                    data, header = None, None
-
-        # remove extracted files
-        if extension=='.zip' and os.path.isdir(path_to_data):
-            shutil.rmtree(path_to_data)
+                            ysh, xsh = img.shape[0], img.shape[1]
+                            csh, channel = 0, None
+
+                        # load data slice by slice
+                        data = np.empty((len(files), ysh, xsh), dtype=img.dtype)
+                        header, image_data_shape = [], []
+                        for k, file_name in enumerate(files):
+                            img, img_header = load(file_name)
+                            if csh==3:
+                                img = rgb2gray(img, channel)
+                            elif csh==1 and channel=='last':
+                                img = img[:,:,0]
+                            elif csh==1 and channel=='first':
+                                img = img[0,:,:]
+                            data[k] = img
+                            header.append(img_header)
+                        header = [header, files, data.dtype]
+                        data = np.swapaxes(data, 1, 2)
+                        data = np.copy(data, order='C')
+                    except Exception as e:
+                        print(e)
+                        data, header = None, None
 
     elif extension == '.mrc':
         try:
@@ -495,34 +488,31 @@ def save_data(path_to_final, final, header=None, final_image_type=None, compress
         simg.CopyInformation(header)
         sitk.WriteImage(simg, path_to_final, useCompression=compress)
     elif final_image_type in ['.zip', 'directory', '']:
-        # make results directory
-        if final_image_type == '.zip':
-            results_dir = BASE_DIR + '/tmp/' + id_generator(40)
-            os.makedirs(results_dir)
-            os.chmod(results_dir, 0o770)
-        else:
-            results_dir = path_to_final
-            if not os.path.isdir(results_dir):
-                os.makedirs(results_dir)
-                os.chmod(results_dir, 0o770)
-        # save data as NC blocks
-        if os.path.splitext(header[1][0])[1] == '.nc':
-            np_to_nc(results_dir, final, header)
-            file_names = header[1]
-        # save data as PNG, TIF, DICOM slices
-        else:
-            header, file_names, final_dtype = header[0], header[1], header[2]
-            final = final.astype(final_dtype)
-            final = np.swapaxes(final, 2, 1)
-            for k, file in enumerate(file_names):
-                save(final[k], results_dir + '/' + os.path.basename(file), header[k])
-        # zip data
-        if final_image_type == '.zip':
-            with zipfile.ZipFile(path_to_final, 'w') as zip:
-                for file in file_names:
-                    zip.write(results_dir + '/' + os.path.basename(file), os.path.basename(file))
-            if os.path.isdir(results_dir):
-                shutil.rmtree(results_dir)
+        with tempfile.TemporaryDirectory() as temp_dir:
+            # make results directory
+            if final_image_type == '.zip':
+                results_dir = temp_dir
+            else:
+                results_dir = path_to_final
+                if not os.path.isdir(results_dir):
+                    os.makedirs(results_dir)
+                    os.chmod(results_dir, 0o770)
+            # save data as NC blocks
+            if os.path.splitext(header[1][0])[1] == '.nc':
+                np_to_nc(results_dir, final, header)
+                file_names = header[1]
+            # save data as PNG, TIF, DICOM slices
+            else:
+                header, file_names, final_dtype = header[0], header[1], header[2]
+                final = final.astype(final_dtype)
+                final = np.swapaxes(final, 2, 1)
+                for k, file in enumerate(file_names):
+                    save(final[k], results_dir + '/' + os.path.basename(file), header[k])
+            # zip data
+            if final_image_type == '.zip':
+                with zipfile.ZipFile(path_to_final, 'w') as zip:
+                    for file in file_names:
+                        zip.write(results_dir + '/' + os.path.basename(file), os.path.basename(file))
     else:
         imageSize = int(final.nbytes * 10e-7)
         bigtiff = True if imageSize > 2000 else False