batoolset 0.1.0__py3-none-any.whl

batoolset/version.py

@@ -0,0 +1,10 @@
+__MAJOR__ = 0
+__MINOR__ = 1
+__MICRO__ = 0
+__RELEASE__ = ''  # a #b  # https://www.python.org/dev/peps/pep-0440/#public-version-identifiers --> alpha beta, ...
+__VERSION__ = ''.join([str(__MAJOR__), '.', str(__MINOR__), '.', str(__MICRO__)])
+__DESCRIPTION__= """An aggregate of functions I find useful"""
+__URL__='https://github.com/baigouy/batoolset'
+
+__EMAIL__ = 'benoit.aigouy@gmail.com'
+__AUTHOR__ = 'Benoit Aigouy'

batoolset/xml/tools.py

@@ -0,0 +1,65 @@
+import xml.etree.ElementTree as ET
+
+from batoolset.files.tools import get_consolidated_filename_from_parent
+
+
+def _replace_filename_tags(file_path):
+    # just a small trick to allow template mode in PyFigures
+    # Parse the XML file
+    tree = ET.parse(file_path)
+    root = tree.getroot()
+
+    # Find the <filename> tags and replace their content with '@template@'
+    for elem in root.iter('filename'):
+        if elem.text and elem.text !='None':
+            elem.text = '""@template@""'
+
+    # Overwrite the original file with the modified XML
+    tree.write(file_path)
+
+
+# def _remove_insets(file_path):
+#     # just a small trick to allow template mode in PyFigures
+#     # Parse the XML file
+#     tree = ET.parse(file_path)
+#     root = tree.getroot()
+#
+#     # Find the <annotations> tag
+#     annotations_tag = root.find('annotations')
+#     print('annotations_tag', annotations_tag)
+#     if annotations_tag is not None:
+#         # Iterate over its children and remove the <image2D> tags
+#         for elem in annotations_tag.iter('Image2D'):
+#             print('removing', elem)
+#             annotations_tag.remove(elem)
+#
+#     # Overwrite the original file with the modified XML
+#     tree.write(file_path)
+
+
+
+
+def _update_filename_of_consolidated_files(file_path, xml_string):
+    # just a small trick to allow template mode in PyFigures
+    # Parse the XML file
+    # tree = ET.parse(file_path)
+    root = ET.fromstring(xml_string)
+    # root = tree.getroot()
+
+    # Find the <filename> tags and replace their content with '@template@'
+    for elem in root.iter('filename'):
+        # elem.text = '""@template@""'
+        if elem.text == 'None':
+            continue
+
+        value = elem.text
+        if isinstance(value, str) and value.startswith('""') and value.endswith('""'):
+            value = value[2:-2]
+            elem.text = f'""{get_consolidated_filename_from_parent(value,file_path)}""'
+
+    # Overwrite the original file with the modified XML
+    # tree.write(file_path)
+    # Convert the modified XML back to a string
+    xml_string = ET.tostring(root, encoding='unicode')  # encoding='unicode' returns a string, otherwise it returns a bytes object
+
+    return xml_string

batoolset/zip_tools/tools.py

@@ -0,0 +1,76 @@
+import gzip
+import shutil
+import os
+import subprocess
+from timeit import default_timer as timer
+from batoolset.files.tools import smart_name_parser
+
+def compress_file_using_python(file_path, output_name=None):
+    """
+    Compresses the specified file using gzip compression.
+
+    Args:
+        file_path (str): The path to the file to be compressed.
+        output_name (str, optional): The name of the compressed output file. If not provided, a default name is generated.
+    """
+    if output_name is None:
+        output_name = os.path.splitext(file_path)[0] + '.gz'
+    os.makedirs(smart_name_parser(output_name, 'parent'), exist_ok=True)
+    with open(file_path, 'rb') as f_in:
+        with gzip.open(output_name, 'wb') as f_out:
+            shutil.copyfileobj(f_in, f_out)
+
+
+def compress_file_3rd_party(file_path, output_path=None):
+    """
+    Compresses the specified file using system gzip compression.
+
+    Args:
+        file_path (str): The path to the file to be compressed.
+        output_path (str, optional): The path to the output file. If not provided, a default path is generated.
+    """
+    if output_path is None:
+        output_path = file_path + '.gz'
+
+    command = ['gzip', '-c', file_path]
+    print('running: ' + ' '.join(command) + ' > ' + output_path)
+    # create dirs if not exist
+    os.makedirs(smart_name_parser(output_path, 'parent'), exist_ok=True)
+    subprocess.run(['gzip', '-c', file_path], stdout=open(output_path, 'wb'))
+
+
+if __name__ == '__main__':
+
+    if True:
+        # do a real compression of a real file
+        start = timer()
+        file_path = '/D/hiC_microC/hiC_data_fub1_n_ctrl/mapped.pairs'
+        output_name = '/D/hiC_microC/hiC_data_fub1_n_ctrl/12-16.txt.gz'
+        compress_file_3rd_party(file_path, output_name)
+        print(timer() - start)
+        import sys
+
+        sys.exit(0)
+
+    if False:
+        # very slow --> only for small files
+        start = timer()
+        file_path = '/D/hiC_microC/hiC_data_fub1_n_ctrl/mapped.txt'
+        compress_file_using_python(file_path)
+        print(timer() - start)
+
+        start = timer()
+        output_name = '/D/hiC_microC/hiC_data_fub1_n_ctrl/tutu/mapped2.txt.gz'
+        compress_file_using_python(file_path, output_name)
+        print(timer() - start)
+
+    if True:
+        file_path = '/D/hiC_microC/hiC_data_fub1_n_ctrl/mapped.txt'
+        output_path = '/D/hiC_microC/hiC_data_fub1_n_ctrl/tutu/mapped2.txt.gz'
+        start = timer()
+        compress_file_3rd_party(file_path, output_path)
+        print(timer() - start)
+
+        start = timer()
+        compress_file_3rd_party(file_path)
+        print(timer() - start)

batoolset-0.1.0.dist-info/LICENSE

@@ -0,0 +1,24 @@
+BSD 2-Clause License
+
+Copyright (c) 2024, baigouy
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

batoolset-0.1.0.dist-info/METADATA

@@ -0,0 +1,45 @@
+Metadata-Version: 2.1
+Name: batoolset
+Version: 0.1.0
+Summary: An aggregate of functions I find useful
+Home-page: https://github.com/baigouy/batoolset
+Author: Benoit Aigouy
+Author-email: benoit.aigouy@gmail.com
+License: BSD
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.7, <3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: czifile
+Requires-Dist: Markdown
+Requires-Dist: matplotlib >=3.5.2
+Requires-Dist: numpy
+Requires-Dist: Pillow >=8.1.2
+Requires-Dist: PyQt6
+Requires-Dist: read-lif
+Requires-Dist: scikit-image >=0.19.3
+Requires-Dist: scipy >=1.7.3
+Requires-Dist: scikit-learn >=1.0.2
+Requires-Dist: tifffile >=2021.11.2
+Requires-Dist: tqdm
+Requires-Dist: natsort
+Requires-Dist: numexpr
+Requires-Dist: urllib3
+Requires-Dist: qtawesome
+Requires-Dist: pandas
+Requires-Dist: numba
+Requires-Dist: elasticdeform
+Requires-Dist: roifile
+Requires-Dist: prettytable
+Requires-Dist: pyperclip
+Requires-Dist: QtPy >=2.1.0
+Requires-Dist: Deprecated
+Requires-Dist: Requests
+Requires-Dist: python-bioformats
+Requires-Dist: python-javabridge
+Requires-Dist: pyautogui
+
+# batoolset
+An aggregate of functions I find useful

batoolset-0.1.0.dist-info/RECORD

@@ -0,0 +1,162 @@
+batoolset/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+batoolset/img.py,sha256=nBs3rCTILhIc6to0buWZfPbPw_-i4zvLZTJERTiws1M,213578
+batoolset/version.py,sha256=enGsc6bOrqD_rOSHpMUabU0j7eh8XkeNP0GdMLh74RI,418
+batoolset/GUI/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+batoolset/GUI/list_gui.py,sha256=nJBf5Pyv47REYb6swga5SfBvi8UuiIcrJZaG36ce0tA,20007
+batoolset/GUI/multi_image_display.py,sha256=UZkFH3yzljsGZmYNdn-ZBlPLZeBa-raQM0FabIkxsXg,41455
+batoolset/GUI/open.py,sha256=oPyi6l6T5Z2TvSTOj4QGuaz3oScGasC5g53edgf0GnQ,12967
+batoolset/GUI/overlay_hints.py,sha256=d1u2cWo6IsWOtqfQ8BTiCgTdBT7KKc_kJ2-NHDCNl0o,1481
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+batoolset/GUI/scrollablepaint.py,sha256=bH8NcIg7Dfm45nF8jV389bVIiQSD7hojINrfTwoXvEo,45382
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+batoolset/command_line/tools.py,sha256=Dw1ohMrmi2pZWH27GcFD4ClOZ0oGL-RO4bBrry4sj8E,541
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+batoolset/dialogs/opensave.py,sha256=cSyReyGOyngPoqKH1Qgs4G_3X4SjQ-cUTPveIVdJw4E,8055
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