pma-python 2.0.0.181__tar.gz → 2.0.0.183__tar.gz

{pma_python-2.0.0.181 → pma_python-2.0.0.183}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pma_python
-Version: 2.0.0.181
+Version: 2.0.0.183
 Summary: Universal viewing of digital microscopy, whole slide imaging and digital pathology data
 Home-page: https://github.com/pathomation/pma_python
 Author: Pathomation

{pma_python-2.0.0.181 → pma_python-2.0.0.183}/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-2.0.0.181 → pma_python-2.0.0.183}/pma_python/core.py

@@ -599,6 +599,7 @@ def analyse_corresponding_slides(sessionPathDict, recursive=False, includeFinger
     """
     Return a pandas DataFrame that indicates which slides exist on which PMA.core instances
     :param dict sessionPathDict: a dictionary that looks e.g. like
+
            {DevSessionID: rootDirAndPath1, ProdSessionID: rootDirAndPath2 }
     :param bool recursive: indicates whether the method should look in sub-directories or not
     """
@@ -825,10 +826,12 @@ def get_zoomlevels_dict(slideRef, sessionID=None, min_number_of_tiles=0):
     """
     Obtain a dictionary with the number of tiles per zoomlevel.
     Information is returned as (x, y, n) tuples per zoomlevel, with
+
         x = number of horizontal tiles,
         y = number of vertical tiles,
         n = total number of tiles at specified zoomlevel (x * y)
-    Use min_number_of_tiles argument to specify that you're only interested in zoomlevels that include at lease a given number of tiles
+
+    Use min_number_of_tiles argument to specify that you're only interested in zoomlevels that include at least a given number of tiles
     """
     zoomlevels = list(range(0, get_max_zoomlevel(slideRef, sessionID) + 1))
     dimensions = [
@@ -1728,7 +1731,8 @@ def add_annotations(slideRef, classification, notes, anns, color="#000000", laye
     :return: An integer representing the annotation id
     :rtype: int
 
-    Example:
+    Example::
+
         anns = []
         annotation = {
             "geometry": string,
@@ -1897,7 +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,
@@ -1921,21 +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)
@@ -1977,8 +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-2.0.0.183/pma_python/version.py

@@ -0,0 +1 @@
+__version__ = '2.0.0.183'

{pma_python-2.0.0.181 → pma_python-2.0.0.183}/pma_python.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pma_python
-Version: 2.0.0.181
+Version: 2.0.0.183
 Summary: Universal viewing of digital microscopy, whole slide imaging and digital pathology data
 Home-page: https://github.com/pathomation/pma_python
 Author: Pathomation

pma_python-2.0.0.181/pma_python/version.py

@@ -1 +0,0 @@
-__version__ = '2.0.0.181'