pma-python 2.0.0.182__tar.gz → 2.0.0.184__tar.gz

{pma_python-2.0.0.182 → pma_python-2.0.0.184}/PKG-INFO

@@ -1,15 +1,16 @@
 Metadata-Version: 2.4
 Name: pma_python
-Version: 2.0.0.182
+Version: 2.0.0.184
 Summary: Universal viewing of digital microscopy, whole slide imaging and digital pathology data
 Home-page: https://github.com/pathomation/pma_python
 Author: Pathomation
 Author-email: info@pathomation.com
 License: https://www.pathomation.com/contact/
-Keywords: wsi whole slide imaging gigapixel microscopy histology pathology
+Keywords: wsi whole slide imaging gigapixel microscopy histology pathology digital pathology pma pma.python pathomation pma.core
 Classifier: Development Status :: 3 - Alpha
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3
+Description-Content-Type: text/markdown
 Requires-Dist: pandas
 Requires-Dist: pillow
 Requires-Dist: requests
@@ -18,6 +19,7 @@ Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
 Dynamic: description
+Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: keywords
 Dynamic: license
@@ -25,22 +27,28 @@ Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary
 
-pma_python is a Python wrapper library for PMA.start (http://free.pathomation.com),
+# pma_python
+pma_python is a Python wrapper library for PMA.core ([https://www.pathomation.com](https://www.pathomation.com)), 
 a universal viewer by Pathomation for whole slide imaging and microscopy.
 
-YOU NEED TO HAVE PMA.START (OR PMA.CORE) RUNNING IN ORDER TO USE THIS
+YOU NEED TO HAVE PMA.core (or PMA.START) RUNNING IN ORDER TO USE THIS
 LIBRARY. PMA_PYTHON IS NOT A STAND-ALONE LIBRARY FOR WSI.
 
 If you're working with
 
-* microscopy data and are you tired of having to use a different library for each vendor specific digital slide format
-* image analysis software and are you looking for a way to have complete control over your algorithms (and not just be able to select those provided for you)
-* novel evaluation methods for histology / pathology and do you just wish there was a way to now automatically evaluate it on 100s of slides (batch processing)
+* microscopy data and are you tired of having to use a different 
+library for each vendor specific digital slide format
+* image analysis software and are you looking for a way to have 
+complete control over your algorithms (and not just be able to 
+select those provided for you)
+* novel evaluation methods for histology / pathology and do you 
+just wish there was a way to now automatically evaluate it on 
+100s of slides (batch processing)
 
-and you're doing all of this in Python, then PMA.start and 
+and you're doing all of this in Python, then PMA.core (or PMA.start) and 
 pma_python are for you! 
 
-PMA.start can be downloaded free of charge from http://free.pathomation.com
+PMA.start can be downloaded from [https://www.pathomation.com/pmastart](https://www.pathomation.com/pmastart)
 
 With pma_python, you can inspect and navigate any type of 
 microscopic imaging file format available. Whether you have 
@@ -72,5 +80,19 @@ The following vendor formats are currently supported:
 * Perkin Elmer (.qptiff)
 
 The most up to date list with supported file formats can be found at
-http://free.pathomation.com/formats
+[http://www.pathomation.com/formats](https://www.pathomation.com/formats)
 
+## Installation from source
+To install from pypi
+```sh
+pip install pma_python
+```
+To upgrade an already existing version from pypi
+```sh
+pip install --upgrade pma_python
+```
+
+## How to use
+```python
+>>> from pma_python import *
+```

{pma_python-2.0.0.182 → pma_python-2.0.0.184}/README.md

@@ -1,8 +1,8 @@
 # pma_python
-pma_python is a Python wrapper library for PMA.start (http://free.pathomation.com), 
+pma_python is a Python wrapper library for PMA.core ([https://www.pathomation.com](https://www.pathomation.com)), 
 a universal viewer by Pathomation for whole slide imaging and microscopy.
 
-YOU NEED TO HAVE PMA.START (OR PMA.CORE) RUNNING IN ORDER TO USE THIS
+YOU NEED TO HAVE PMA.core (or PMA.START) RUNNING IN ORDER TO USE THIS
 LIBRARY. PMA_PYTHON IS NOT A STAND-ALONE LIBRARY FOR WSI.
 
 If you're working with
@@ -16,10 +16,10 @@ select those provided for you)
 just wish there was a way to now automatically evaluate it on 
 100s of slides (batch processing)
 
-and you're doing all of this in Python, then PMA.start and 
+and you're doing all of this in Python, then PMA.core (or PMA.start) and 
 pma_python are for you! 
 
-PMA.start can be downloaded free of charge from http://free.pathomation.com
+PMA.start can be downloaded from [https://www.pathomation.com/pmastart](https://www.pathomation.com/pmastart)
 
 With pma_python, you can inspect and navigate any type of 
 microscopic imaging file format available. Whether you have 
@@ -51,7 +51,7 @@ The following vendor formats are currently supported:
 * Perkin Elmer (.qptiff)
 
 The most up to date list with supported file formats can be found at
-http://free.pathomation.com/formats
+[http://www.pathomation.com/formats](https://www.pathomation.com/formats)
 
 ## Installation from source
 To install from pypi

{pma_python-2.0.0.182 → pma_python-2.0.0.184}/pma_python/core.py

@@ -1901,7 +1901,30 @@ def get_annotation_distance(slideRef, layerID, annotationID, sessionID=None, ver
 # **************************************#
 #           === Uploader ===            #
 # **************************************#
+FOUR_GB = 4 * 1024 * 1024 * 1024
 FIVE_GB = 5 * 1024 * 1024 * 1024
+
+def _get_slide_package_size(slide_path: str) -> tuple[int, int]:
+    """Return total bytes and maximum single-file bytes for a slide package."""
+    total_size = 0
+    max_size = 0
+
+    files = [slide_path]
+    slide_name_no_ext = os.path.splitext(os.path.basename(slide_path))[0]
+    slide_dir = os.path.join(os.path.dirname(slide_path), slide_name_no_ext)
+
+    if os.path.isdir(slide_dir):
+        for root, _, filenames in os.walk(slide_dir):
+            for filename in filenames:
+                files.append(os.path.join(root, filename))
+
+    for filepath in files:
+        size = os.stat(filepath).st_size
+        total_size += size
+        max_size = max(max_size, size)
+
+    return total_size, max_size
+
 async def upload(
         *,
         pma_core_url: str,
@@ -1925,21 +1948,10 @@ async def upload(
     # ================================
     # CALCULATE TOTAL SLIDE SIZE
     # ================================
-    total_size = 0
-
-    # main file size
-    total_size += os.stat(slide_path).st_size
-
-    # possible slide folder (multi-files slides)
-    slide_name_no_ext = os.path.splitext(os.path.basename(slide_path))[0]
-    slide_dir = os.path.join(os.path.dirname(slide_path), slide_name_no_ext)
-
-    if os.path.isdir(slide_dir):
-        for root, _, files in os.walk(slide_dir):
-            for f in files:
-                total_size += os.stat(os.path.join(root, f)).st_size
+    total_size, max_file_size = _get_slide_package_size(slide_path)
 
     print("Total slide size:", round(total_size / (1024 ** 3), 2), "GB")
+    print("Largest single file:", round(max_file_size / (1024 ** 3), 2), "GB")
 
     # ================================
     # CHECK UPLOAD TYPE (PRE-FLIGHT)
@@ -1981,8 +1993,8 @@ async def upload(
                 progress_callback=progress_callback
             )
 
-        # Otherwise fallback to size logic
-        if total_size < FIVE_GB:
+        # Otherwise choose based on total package size or safe single-request cap
+        if total_size < FOUR_GB and max_file_size < FIVE_GB:
             print("Using SMALL file uploader")
 
             return upload_legacy(

pma_python-2.0.0.184/pma_python/version.py

@@ -0,0 +1 @@
+__version__ = '2.0.0.184'

{pma_python-2.0.0.182 → pma_python-2.0.0.184}/pma_python.egg-info/PKG-INFO

@@ -1,15 +1,16 @@
 Metadata-Version: 2.4
 Name: pma_python
-Version: 2.0.0.182
+Version: 2.0.0.184
 Summary: Universal viewing of digital microscopy, whole slide imaging and digital pathology data
 Home-page: https://github.com/pathomation/pma_python
 Author: Pathomation
 Author-email: info@pathomation.com
 License: https://www.pathomation.com/contact/
-Keywords: wsi whole slide imaging gigapixel microscopy histology pathology
+Keywords: wsi whole slide imaging gigapixel microscopy histology pathology digital pathology pma pma.python pathomation pma.core
 Classifier: Development Status :: 3 - Alpha
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3
+Description-Content-Type: text/markdown
 Requires-Dist: pandas
 Requires-Dist: pillow
 Requires-Dist: requests
@@ -18,6 +19,7 @@ Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
 Dynamic: description
+Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: keywords
 Dynamic: license
@@ -25,22 +27,28 @@ Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary
 
-pma_python is a Python wrapper library for PMA.start (http://free.pathomation.com),
+# pma_python
+pma_python is a Python wrapper library for PMA.core ([https://www.pathomation.com](https://www.pathomation.com)), 
 a universal viewer by Pathomation for whole slide imaging and microscopy.
 
-YOU NEED TO HAVE PMA.START (OR PMA.CORE) RUNNING IN ORDER TO USE THIS
+YOU NEED TO HAVE PMA.core (or PMA.START) RUNNING IN ORDER TO USE THIS
 LIBRARY. PMA_PYTHON IS NOT A STAND-ALONE LIBRARY FOR WSI.
 
 If you're working with
 
-* microscopy data and are you tired of having to use a different library for each vendor specific digital slide format
-* image analysis software and are you looking for a way to have complete control over your algorithms (and not just be able to select those provided for you)
-* novel evaluation methods for histology / pathology and do you just wish there was a way to now automatically evaluate it on 100s of slides (batch processing)
+* microscopy data and are you tired of having to use a different 
+library for each vendor specific digital slide format
+* image analysis software and are you looking for a way to have 
+complete control over your algorithms (and not just be able to 
+select those provided for you)
+* novel evaluation methods for histology / pathology and do you 
+just wish there was a way to now automatically evaluate it on 
+100s of slides (batch processing)
 
-and you're doing all of this in Python, then PMA.start and 
+and you're doing all of this in Python, then PMA.core (or PMA.start) and 
 pma_python are for you! 
 
-PMA.start can be downloaded free of charge from http://free.pathomation.com
+PMA.start can be downloaded from [https://www.pathomation.com/pmastart](https://www.pathomation.com/pmastart)
 
 With pma_python, you can inspect and navigate any type of 
 microscopic imaging file format available. Whether you have 
@@ -72,5 +80,19 @@ The following vendor formats are currently supported:
 * Perkin Elmer (.qptiff)
 
 The most up to date list with supported file formats can be found at
-http://free.pathomation.com/formats
+[http://www.pathomation.com/formats](https://www.pathomation.com/formats)
 
+## Installation from source
+To install from pypi
+```sh
+pip install pma_python
+```
+To upgrade an already existing version from pypi
+```sh
+pip install --upgrade pma_python
+```
+
+## How to use
+```python
+>>> from pma_python import *
+```

{pma_python-2.0.0.182 → pma_python-2.0.0.184}/pma_python.egg-info/SOURCES.txt

@@ -1,5 +1,4 @@
 README.md
-long_desc.txt
 setup.py
 pma_python/__init__.py
 pma_python/control.py

{pma_python-2.0.0.182 → pma_python-2.0.0.184}/setup.py

@@ -24,17 +24,18 @@ def extract_version(v):
 setup(name='pma_python',
       version=extract_version(read("pma_python/version.py")),
       description='Universal viewing of digital microscopy, whole slide imaging and digital pathology data',
-      long_description=read('long_desc.txt'),
+      long_description=read('README.md'),
+      long_description_content_type='text/markdown',
       url='https://github.com/pathomation/pma_python',
       author='Pathomation',
       author_email='info@pathomation.com',
       license='https://www.pathomation.com/contact/',
       packages=['pma_python'],
-      data_files=[('', ['long_desc.txt'])],
+      data_files=[('', ['README.md'])],
       classifiers=[
           'Development Status :: 3 - Alpha',
           'Programming Language :: Python :: 3'],
-      keywords='wsi whole slide imaging gigapixel microscopy histology pathology',
+      keywords='wsi whole slide imaging gigapixel microscopy histology pathology digital pathology pma pma.python pathomation pma.core',
       install_requires=['pandas', 'pillow', 'requests', 'requests_toolbelt'],
       python_requires='>=3',  # assume this only works in Python 3
       zip_safe=False)

pma_python-2.0.0.182/long_desc.txt

@@ -1,49 +0,0 @@
-pma_python is a Python wrapper library for PMA.start (http://free.pathomation.com),
-a universal viewer by Pathomation for whole slide imaging and microscopy.
-
-YOU NEED TO HAVE PMA.START (OR PMA.CORE) RUNNING IN ORDER TO USE THIS
-LIBRARY. PMA_PYTHON IS NOT A STAND-ALONE LIBRARY FOR WSI.
-
-If you're working with
-
-* microscopy data and are you tired of having to use a different library for each vendor specific digital slide format
-* image analysis software and are you looking for a way to have complete control over your algorithms (and not just be able to select those provided for you)
-* novel evaluation methods for histology / pathology and do you just wish there was a way to now automatically evaluate it on 100s of slides (batch processing)
-
-and you're doing all of this in Python, then PMA.start and 
-pma_python are for you! 
-
-PMA.start can be downloaded free of charge from http://free.pathomation.com
-
-With pma_python, you can inspect and navigate any type of 
-microscopic imaging file format available. Whether you have 
-macroscopic observations, whole slide imaging data, or fluorescent 
-snapshot observations, we can bring it all into Python now.
-
-The following vendor formats are currently supported:
-
-* TIFF (.tif, .tiff) with JPEG, JPEG2000, LZW, Deflate, Raw, RLE		
-* JPEG (.jpeg, .jpg)
-* JPEG 2000 (.jp2)
-* PNG (.png)
-* Olympus VSI (.vsi) with lossless JPEG, JPEG, Raw
-* Ventana / Roche BIF (.bif)
-* Hamamatsu (.vms, .ndpi, .dcm) with JPEG, JPEG2000
-* Huron Technologies (.tif)
-* 3DHistech (.mrxs) with JPEG, PNG, BMP
-* Aperio / Leica (.svs, .cws, .scn, .lif, DICOMDIR) with JPEG, JPEG2000
-* Carl Zeiss (.zvi, .czi, .lsm) with Raw, PNG, JPEG, LZW, Deflate, JPEG2000	
-* Open Microscopy Environment OME-TIFF (.tf2, .tf8, .btf, .ome.tif)
-* Nikon (.nd2, .tiff) with Deflate, JPEG, JPEG2000, LZW, Deflate, Raw, RLE	
-* Philips (.tif) with JPEG, JPEG2000, LZW, Deflate, Raw, RLE		
-* Sakura (.svslide) with JPEG(sqlite2, sqlite3, mssql)
-* Menarini (.ini) with Raw
-* Motic (.mds) 
-* Zoomify (.zif) with JPEG, JPEG2000, LZW, Deflate, Raw, RLE
-* SmartZoom	(.szi) with JPEG, BMP
-* Objective Imaging / Glissano (.sws)
-* Perkin Elmer (.qptiff)
-
-The most up to date list with supported file formats can be found at
-http://free.pathomation.com/formats
-

pma_python-2.0.0.182/pma_python/version.py

@@ -1 +0,0 @@
-__version__ = '2.0.0.182'