dcnum 0.23.1__py3-none-any.whl → 0.23.2__py3-none-any.whl

dcnum/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.23.1'
-__version_tuple__ = version_tuple = (0, 23, 1)
+__version__ = version = '0.23.2'
+__version_tuple__ = version_tuple = (0, 23, 2)

dcnum/logic/ctrl.py

@@ -1,6 +1,7 @@
 import collections
 import datetime
 import hashlib
+import importlib
 import json
 import logging
 from logging.handlers import QueueListener
@@ -430,6 +431,16 @@ class DCNumJobRunner(threading.Thread):
                                  "build": ", ".join(platform.python_build()),
                                  "implementation":
                                      platform.python_implementation(),
+                                 "libraries": get_library_versions_dict([
+                                     "cv2",
+                                     "h5py",
+                                     "mahotas",
+                                     "numba",
+                                     "numpy",
+                                     "scipy",
+                                     "skimage",
+                                     "torch",
+                                 ]),
                                  "version": platform.python_version(),
                                  },
                              "system": {
@@ -780,6 +791,19 @@ class DCNumJobRunner(threading.Thread):
         self.logger.info("Finished segmentation and feature extraction")
 
 
+def get_library_versions_dict(library_name_list):
+    version_dict = {}
+    for library_name in library_name_list:
+        try:
+            lib = importlib.import_module(library_name)
+        except BaseException:
+            version = None
+        else:
+            version = lib.__version__
+        version_dict[library_name] = version
+    return version_dict
+
+
 def join_thread_helper(thr, timeout, retries, logger, name):
     for _ in range(retries):
         thr.join(timeout=timeout)

dcnum/logic/job.py

@@ -182,3 +182,25 @@ class DCNumPipelineJob:
         if len(ret) == 1:
             ret = ret[0]
         return ret
+
+    def validate(self):
+        """Make sure the pipeline will run given the job kwargs
+
+        Returns
+        -------
+        True:
+            for testing convenience
+
+        Raises
+        ------
+        dcnum.segm.SegmenterNotApplicableError:
+            the segmenter is incompatible with the input path
+        """
+        # Check segmenter applicability applicability
+        seg_cls = get_available_segmenters()[self.kwargs["segmenter_code"]]
+        with HDF5Data(self.kwargs["path_in"]) as hd:
+            seg_cls.validate_applicability(
+                segmenter_kwargs=self.kwargs["segmenter_kwargs"],
+                logs=hd.logs,
+                meta=hd.meta)
+        return True

dcnum/segm/segm_torch/__init__.py

@@ -1,16 +1,20 @@
 import importlib
+import warnings
 
 try:
     torch = importlib.import_module("torch")
     req_maj = 2
-    req_min = 3
+    req_min = 2
     ver_tuple = torch.__version__.split(".")
     act_maj = int(ver_tuple[0])
     act_min = int(ver_tuple[1])
     if act_maj < req_maj or (act_maj == req_maj and act_min < req_min):
-        raise ValueError(f"Your PyTorch version {act_maj}.{act_min} is not "
-                         f"supported, please update to at least "
-                         f"{req_maj}.{req_min}")
+        warnings.warn(f"Your PyTorch version {act_maj}.{act_min} is "
+                      f"not supported, please update to at least "
+                      f"{req_maj}.{req_min} to use dcnum's PyTorch"
+                      f"segmenters")
+        raise ImportError(
+            f"Could not find PyTorch {req_maj}.{req_min}")
 except ImportError:
     pass
 else:

{dcnum-0.23.1.dist-info → dcnum-0.23.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.23.1
+Version: 0.23.2
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>
@@ -26,7 +26,7 @@ Requires-Dist: opencv-python-headless
 Requires-Dist: scikit-image
 Requires-Dist: scipy >=1.8.0
 Provides-Extra: torch
-Requires-Dist: torch >=2.3 ; extra == 'torch'
+Requires-Dist: torch >=2.2 ; extra == 'torch'
 
 |dcnum|
 =======

{dcnum-0.23.1.dist-info → dcnum-0.23.2.dist-info}/RECORD

@@ -1,5 +1,5 @@
 dcnum/__init__.py,sha256=hcawIKS7utYiOyVhOAX9t7K3xYzP1b9862VV0b6qSrQ,74
-dcnum/_version.py,sha256=FvSfCBPqaPzqv_nSHIaBJNolXopVkF1cRxifqhCXk4g,413
+dcnum/_version.py,sha256=GmxD5FOokmDsV6mmMcLj8aWXLveU0OeVRPLBT4HJfDk,413
 dcnum/feat/__init__.py,sha256=jUJYWTD3VIoDNKrmryXbjHb1rGwYtK4b7VPWihYgUoo,325
 dcnum/feat/event_extractor_manager_thread.py,sha256=5HdCQCywyQ5QC56AMjSqCroqif9oOFyiSFWCe07JojM,7820
 dcnum/feat/gate.py,sha256=Yhxq80JoRMmQzBxl35C8NT91c9QcmQa-EIKLuxK6WvE,7221
@@ -20,8 +20,8 @@ dcnum/feat/feat_texture/__init__.py,sha256=6StM9S540UVtdFFR3bHa7nfCTomeVdoo7Uy9C
 dcnum/feat/feat_texture/common.py,sha256=COXHpXS-7DMouGu3WF83I76L02Sr7P9re4lxajh6g0E,439
 dcnum/feat/feat_texture/tex_all.py,sha256=_5H3sXYRN0Uq2eUHn3XUyEHkU_tncEqbqJTC-HZcnGY,5198
 dcnum/logic/__init__.py,sha256=7J3GrwJInNQbrLk61HRIV7X7p69TAIbMYpR34hh6u14,177
-dcnum/logic/ctrl.py,sha256=FyVlizHOIaIGMqINvM-outPywAQU0-5NM7t1dEDml4c,35332
-dcnum/logic/job.py,sha256=H1uDZ1nnNHNWWCe6mS8OWB0Uxc6XUKLISx5xExeplZY,7015
+dcnum/logic/ctrl.py,sha256=9QFNudpaZfL3hKYskOgMiscOOQPU2xbupVzI23aNWiE,36193
+dcnum/logic/job.py,sha256=9BN2WjYqjjJuLnfNZAtQ2Nn47Glo2jVrivDodGJoqlQ,7713
 dcnum/logic/json_encoder.py,sha256=cxMnqisbKEVf-rVcw6rK2BBAb6iz_hKFaGl81kK36lQ,571
 dcnum/meta/__init__.py,sha256=AVqRgyKXO1orKnE305h88IBvoZ1oz6X11HN1WP5nGvg,60
 dcnum/meta/paths.py,sha256=J_ikeHzd7gEeRgAKjuayz3x6q4h1fOiDadM-ZxhAGm4,1053
@@ -37,7 +37,7 @@ dcnum/segm/segmenter.py,sha256=FWLFDBR-x_85ku2rObA2F-QBrM4IUaUL-YHChLagVvM,14902
 dcnum/segm/segmenter_manager_thread.py,sha256=frM0sMxC7f7TQiFjmpRxuwG2kUBFpW1inV8dtpADHiI,5924
 dcnum/segm/segmenter_mpo.py,sha256=o6mQlITHgEWvQt9v6oCWwAcZUvxE7MOeLE9DFManzpY,13757
 dcnum/segm/segmenter_sto.py,sha256=e6MtN_RWusA0wTExV-FLGpDXNJs1CbSyXcSdWUPBMvM,3959
-dcnum/segm/segm_torch/__init__.py,sha256=re9jVLYvV1GgC7J5vx2LHKeFYVZPpiwubecAV9f_2kA,670
+dcnum/segm/segm_torch/__init__.py,sha256=DtUqJTbj7ybrTbXlwHq1Y4SCzi22rMW9Cus6wX-iU-A,822
 dcnum/segm/segm_torch/segm_torch_base.py,sha256=G9AhVyD6LkAmk0tkbYnJUSpvcj3_HYf0uqfILZQsyus,4479
 dcnum/segm/segm_torch/segm_torch_mpo.py,sha256=N01dVXai_4eIGfHJrPjg5C2Bkyq1TOeXeJhw3YbGidw,2504
 dcnum/segm/segm_torch/segm_torch_sto.py,sha256=PTOJrP_FkaxZZul8lM4VA2HL3KyxrheDDWWdJbmJdiw,3393
@@ -48,8 +48,8 @@ dcnum/write/__init__.py,sha256=QvWHeZmjHI18i-YlGYuzN3i7dVWY9UCReKchrJ-gif0,260
 dcnum/write/deque_writer_thread.py,sha256=ao7F1yrVKyufgC4rC0Y2_Vt7snuT6KpI7W2qVxcjdhk,1994
 dcnum/write/queue_collector_thread.py,sha256=d_WfdsZdFnFsiAY0zVMwUlA4juIMeiWYmE_-rezBQCE,11734
 dcnum/write/writer.py,sha256=e6J8YVqhS7kzkpPIMoDMokJpqSy1WWNdOrwaJof1oVc,15601
-dcnum-0.23.1.dist-info/LICENSE,sha256=YRChA1C8A2E-amJbudwMcbTCZy_HzmeY0hMIvduh1MM,1089
-dcnum-0.23.1.dist-info/METADATA,sha256=NL79bLTjTqm5R4HW0TNcVZ9YXqbxH7Xcfl6xuk-hfw4,2280
-dcnum-0.23.1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-dcnum-0.23.1.dist-info/top_level.txt,sha256=Hmh38rgG_MFTVDpUDGuO2HWTSq80P585Het4COQzFTg,6
-dcnum-0.23.1.dist-info/RECORD,,
+dcnum-0.23.2.dist-info/LICENSE,sha256=YRChA1C8A2E-amJbudwMcbTCZy_HzmeY0hMIvduh1MM,1089
+dcnum-0.23.2.dist-info/METADATA,sha256=HLyOwJN79qpOR5yXjWtt5XjkT3nRQujPlxuvQZSYLbI,2280
+dcnum-0.23.2.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+dcnum-0.23.2.dist-info/top_level.txt,sha256=Hmh38rgG_MFTVDpUDGuO2HWTSq80P585Het4COQzFTg,6
+dcnum-0.23.2.dist-info/RECORD,,