batoolset 0.1.0__py3-none-any.whl

batoolset/IJ_ROIs/tools.py

@@ -0,0 +1,40 @@
+import os
+
+def save_IJ_ROIs_or_overlays(rois, output_filename):
+    """
+    Saves ImageJ ROIs or overlays to a file.
+
+    Args:
+        rois (list): List of ROIs or overlays to be saved.
+        output_filename (str): Output filename for saving the ROIs.
+
+    Returns:
+        None
+    """
+
+    # Check the number of ROIs
+    if len(rois) > 1:
+        # If there are multiple ROIs, check if the output filename ends with '.zip'.
+        # If not, append '.zip' to the output filename.
+        if not output_filename.lower().endswith('.zip'):
+            output_filename += '.zip'
+
+        # Check if the output file already exists and delete it if it does.
+        if os.path.exists(output_filename):
+            os.remove(output_filename)
+    else:
+        # If there is only one ROI, check if the output filename ends with '.roi'.
+        # If not, append '.roi' to the output filename.
+        if not output_filename.lower().endswith('.roi'):
+            output_filename += '.roi'
+
+    # Check if the ROIs list is not empty or None
+    if rois is not None and rois:
+        # Iterate over each ROI
+        for roi in rois:
+            # Save the ROI to the output filename
+            roi.tofile(output_filename)
+
+
+if __name__ == '__main__':
+    pass

batoolset/PATH/tools.py

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+import sys
+import os
+def add_folder_to_python_path(folder_path):
+    """
+    Add a folder to the Python path.
+
+    Parameters:
+    - folder_path (str): The path of the folder to be added to the Python path.
+    """
+    if isinstance(folder_path, str):
+        sys.path.append(folder_path)
+    else:
+        # assume it's a list
+        for path in folder_path:
+            add_folder_to_python_path(path)
+
+def add_folder_to_system_path(folder_path):
+    """
+    Add a folder to the system PATH.
+
+    Parameters:
+    - folder_path (str): The path of the folder to be added to the system PATH.
+    """
+    if isinstance(folder_path, str):
+        os.environ['PATH'] += os.pathsep + folder_path
+    else:
+        # assume it's a list
+        for path in folder_path:
+            add_folder_to_system_path(path)
+
+def find_bin_folders(root_folder):
+    bin_folders = []
+
+    # Walk through the directory tree
+    for foldername, subfolders, filenames in os.walk(root_folder):
+        # Check if 'bin' is in the subfolders
+        if 'bin' in subfolders:
+            bin_folders.append(os.path.join(foldername, 'bin'))
+
+    return bin_folders
+
+def add_epyseg_to_sys_path(file=None, print_only=False):
+    # if print_only does not execute the command --> just gets the appropriate text --> print_only creates a portable code that will always work!!!
+    # NB THIS NEEDS BE COPIED UNDER EVERY STUFF THAT NEEDS BE EXECUTED ALONE FROM COMMAND LINE --> THIS CODE NEEDS BE CUT AND PASTE AND CANNOT BE DIRECTLY COPIED THOUGH
+    if file is None:
+        epyseg_path = __file__
+    else:
+        epyseg_path = file
+
+    batoolset_path = __file__.split('epyseg_pkg')[0] + 'batoolset_pkg/'
+    pyfigures_path = __file__.split('epyseg_pkg')[0] + 'pyfigures_pkg/'
+    epyseg_path = __file__.split('epyseg_pkg')[0] + 'epyseg_pkg/'
+    dev_path = __file__.split('epyseg_pkg')[0] + 'dev/'
+
+    if not print_only:
+        sys.path.append(epyseg_path)
+        sys.path.append(batoolset_path)
+        sys.path.append(pyfigures_path)
+        sys.path.append(epyseg_path)
+        sys.path.append(dev_path)
+    else:
+        raise Exception('need a fix')
+        command = '###### add the commands below to the beginning of your python file: ######\n'
+        command += 'import sys\n'
+        # command +=f'epyseg_path = \'{epyseg_path}\'\n'
+        command += f'epyseg_path = __file__\n'
+        command += f'epyseg_path = epyseg_path.split(\'epyseg_pkg\')[0] + \'epyseg_pkg/\'\n'
+        command += 'sys.path.append(epyseg_path)\n'
+        command += '###### end commands ######\n'
+        print(command)
+        return command
+    # add_folder_to_system_path(epyseg_path)
+
+if __name__ == '__main__':
+    # TODO --> make it generate also the code to be put at the top of
+    print(os.cpu_count()-1)
+    print(find_bin_folders('/home/aigouy/mon_prog/Python/epyseg_pkg/personal/hiC_microC_tmp/blast_executables/'))
+    # add_epyseg_to_sys_path()
+    add_epyseg_to_sys_path(print_only=True) # prints the code to copy to the beginning of .py files to get them to run irrespective of the environment