dcnum 0.17.0__py3-none-any.whl → 0.23.2__py3-none-any.whl

dcnum/write/writer.py

@@ -1,7 +1,7 @@
 import hashlib
 import json
 import pathlib
-from typing import List
+from typing import Dict, List
 import warnings
 
 import h5py
@@ -17,9 +17,39 @@ class CreatingFileWithoutBasinWarning(UserWarning):
 
 
 class HDF5Writer:
-    def __init__(self, path, mode="a", ds_kwds=None):
-        """Write deformability cytometry HDF5 data"""
-        self.h5 = h5py.File(path, mode=mode, libver="latest")
+    def __init__(self,
+                 # TODO: make this a mandatory argument when `path` is
+                 #       properly removed
+                 obj: h5py.File | pathlib.Path | str = None,
+                 mode: str = "a",
+                 ds_kwds: Dict = None,
+                 path: pathlib.Path | str = None,
+                 ):
+        """Write deformability cytometry HDF5 data
+
+        Parameters
+        ----------
+        obj: h5py.File | pathlib.Path | str
+            object to instantiate the writer from; If this is already
+            a :class:`h5py.File` object, then it is used, otherwise the
+            argument is passed to :class:`h5py.File`
+        mode: str
+            opening mode when using :class:`h5py.File`
+        ds_kwds: Dict
+            keyword arguments with which to initialize new Datasets
+            (e.g. compression)
+        """
+        if path is not None:
+            obj = path
+            warnings.warn("The `path` keyword argument is deprecated, use "
+                          "`obj` instead",
+                          DeprecationWarning)
+        if isinstance(obj, h5py.File):
+            self.h5 = obj
+            self.h5_owned = False
+        else:
+            self.h5 = h5py.File(obj, mode=mode, libver="latest")
+            self.h5_owned = True
         self.events = self.h5.require_group("events")
         ds_kwds = set_default_filter_kwargs(ds_kwds)
         self.ds_kwds = ds_kwds
@@ -31,7 +61,9 @@ class HDF5Writer:
         self.close()
 
     def close(self):
-        self.h5.close()
+        self.h5.flush()
+        if self.h5_owned:
+            self.h5.close()
 
     @staticmethod
     def get_best_nd_chunks(item_shape, feat_dtype=np.float64):
@@ -83,6 +115,7 @@ class HDF5Writer:
                     paths: List[str | pathlib.Path],
                     features: List[str] = None,
                     description: str | None = None,
+                    mapping: np.ndarray = None
                     ):
         """Write an HDF5-based file basin
 
@@ -96,6 +129,9 @@ class HDF5Writer:
             list of features provided by `paths`
         description: str
             optional string describing the basin
+        mapping: 1D array
+            integer array with indices that map the basin dataset
+            to this dataset
         """
         bdat = {
             "description": description,
@@ -104,8 +140,38 @@ class HDF5Writer:
             "paths": [str(pp) for pp in paths],
             "type": "file",
         }
+        # Explicit features stored in basin file
         if features is not None and len(features):
             bdat["features"] = features
+        # Mapped basin information
+        if mapping is not None:
+            events = self.h5.require_group("events")
+            # Reserve a mapping feature for this dataset
+            for ii in range(10):  # basinmap0 to basinmap9
+                bm_cand = f"basinmap{ii}"
+                if bm_cand in events:
+                    # There is a basin mapping defined in the file. Check
+                    # whether it is identical to ours.
+                    if np.all(events[bm_cand] == mapping):
+                        # Great, we are done here.
+                        feat_basinmap = bm_cand
+                        break
+                    else:
+                        # This mapping belongs to a different basin,
+                        # try the next mapping.
+                        continue
+                else:
+                    # The mapping is not defined in the dataset, and we may
+                    # write it to a new feature.
+                    feat_basinmap = bm_cand
+                    self.store_feature_chunk(feat=feat_basinmap, data=mapping)
+                    break
+            else:
+                raise ValueError(
+                    "You have exhausted the usage of mapped basins for "
+                    "the current dataset. Please revise your analysis "
+                    "pipeline.")
+            bdat["mapping"] = feat_basinmap
         bstring = json.dumps(bdat, indent=2)
         # basin key is its hash
         key = hashlib.md5(bstring.encode("utf-8",
@@ -234,6 +300,63 @@ def create_with_basins(
                            )
 
 
+def copy_features(h5_src: h5py.File,
+                  h5_dst: h5py.File,
+                  features: List[str],
+                  mapping: np.ndarray = None,
+                  ):
+    """Copy feature data from one HDF5 file to another
+
+    The feature must not exist in the destination file.
+
+    Parameters
+    ----------
+    h5_src: h5py.File
+        Input HDF5File containing `features` in the "events" group
+    h5_dst: h5py.File
+        Output HDF5File opened in write mode not containing `features`
+    features: List[str]
+        List of features to copy from source to destination
+    mapping: 1D array
+        If given, contains indices in the input file that should be
+        written to the output file. If set to None, all features are written.
+    """
+    ei = h5_src["events"]
+    eo = h5_dst.require_group("events")
+    # This is the size of the output dataset
+    size = h5_dst.attrs["experiment:event count"]
+    hw = HDF5Writer(h5_dst)
+    for feat in features:
+        if feat in eo:
+            raise ValueError(f"Output file {h5_dst.filename} already contains "
+                             f"the feature {feat}.")
+        if not isinstance(ei[feat], h5py.Dataset):
+            raise NotImplementedError(
+                f"Only dataset-based features are supported here, not {feat}")
+        if mapping is None:
+            # Just copy the data as-is.
+            h5py.h5o.copy(src_loc=ei.id,
+                          src_name=feat.encode(),
+                          dst_loc=eo.id,
+                          dst_name=feat.encode(),
+                          )
+        else:
+            # Perform mapping and store the features in chunks to keep
+            # memory usage down.
+            dsi = ei[feat]
+            chunk_size = hw.get_best_nd_chunks(dsi[0].shape, dsi.dtype)[0]
+            start = 0
+            while start < size:
+                chunk_idx = mapping[start:start + chunk_size]
+                # h5py only supports indexing in increasing order
+                chunk_unique, order = np.unique(chunk_idx, return_inverse=True)
+                data_unique = dsi[chunk_unique]
+                data = data_unique[order]
+                hw.store_feature_chunk(feat, data)
+                # increment start
+                start += chunk_size
+
+
 def copy_metadata(h5_src: h5py.File,
                   h5_dst: h5py.File,
                   copy_basins=True):

{dcnum-0.17.0.dist-info → dcnum-0.23.2.dist-info}/METADATA

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.17.0
+Version: 0.23.2
 Summary: numerics toolbox for imaging deformability cytometry
-Author: Maximilian Schlögel, Paul Müller
+Author: Maximilian Schlögel, Paul Müller, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>
 License: MIT
 Project-URL: source, https://github.com/DC-Analysis/dcnum
@@ -25,6 +25,8 @@ Requires-Dist: numpy >=1.21
 Requires-Dist: opencv-python-headless
 Requires-Dist: scikit-image
 Requires-Dist: scipy >=1.8.0
+Provides-Extra: torch
+Requires-Dist: torch >=2.2 ; extra == 'torch'
 
 |dcnum|
 =======

dcnum-0.23.2.dist-info/RECORD

@@ -0,0 +1,55 @@
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+dcnum/_version.py,sha256=GmxD5FOokmDsV6mmMcLj8aWXLveU0OeVRPLBT4HJfDk,413
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+dcnum/feat/gate.py,sha256=Yhxq80JoRMmQzBxl35C8NT91c9QcmQa-EIKLuxK6WvE,7221
+dcnum/feat/queue_event_extractor.py,sha256=0ncTQleT1sfc98zYkFuZWxU-akecfTrW6-OOU3z-d8o,15698
+dcnum/feat/feat_background/__init__.py,sha256=OTmMuazHNaSrZb2XW4cnJ6PlgJLbKrPbaidpEixYa0A,341
+dcnum/feat/feat_background/base.py,sha256=A-K3qlJ0ABFBGm5eMKYcNCC7ktFAInSm0eR3N3DHQZY,7963
+dcnum/feat/feat_background/bg_copy.py,sha256=PK8x4_Uph-_A6uszZC5uhe1gD1dSRdHnDMEsN0HSGHA,1034
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+dcnum/feat/feat_background/bg_sparse_median.py,sha256=ab7Boj7cmr6PBdTbyWTj_yNNJSfuowr7u-iSGW989WI,20709
+dcnum/feat/feat_brightness/__init__.py,sha256=o6AebVlmydwNgVF5kW6ITqJyFreoKrU3Ki_3EC8If-s,155
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+dcnum/feat/feat_contour/__init__.py,sha256=Td4Hs47kUgJj0VXm3q5ofXhaUWr9QTfVgbwh5EELA-I,163
+dcnum/feat/feat_contour/contour.py,sha256=_qyHCGvylVxruMWafvVbVOzhWGXLoFi10LReNxGcWhY,463
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+dcnum/feat/feat_contour/volume.py,sha256=xVHWtv6USUHJZ5dM1Ur7fI7OwoPT5N2Ps0gKVWylfl8,6639
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+dcnum/logic/__init__.py,sha256=7J3GrwJInNQbrLk61HRIV7X7p69TAIbMYpR34hh6u14,177
+dcnum/logic/ctrl.py,sha256=9QFNudpaZfL3hKYskOgMiscOOQPU2xbupVzI23aNWiE,36193
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+dcnum/logic/json_encoder.py,sha256=cxMnqisbKEVf-rVcw6rK2BBAb6iz_hKFaGl81kK36lQ,571
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+dcnum/meta/paths.py,sha256=J_ikeHzd7gEeRgAKjuayz3x6q4h1fOiDadM-ZxhAGm4,1053
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+dcnum/read/hdf5_data.py,sha256=Yyq02UTILc5ZgIQXpR9Y0wuX2WT8s0g23PraI7KxmJY,23489
+dcnum/read/mapped.py,sha256=UryArlrIsHxjOyimBL2Nooi3r73zuGtnGdqdxa6PK_g,3076
+dcnum/segm/__init__.py,sha256=9cLEAd3JWE8IGqDHV-eSDIYOGBfOepd8OcebtNs8Omk,309
+dcnum/segm/segm_thresh.py,sha256=iVhvIhzO0Gw0t3rXOgH71rOI0CNjJJQq4Gg6BulUhK8,948
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+dcnum/segm/segmenter_sto.py,sha256=e6MtN_RWusA0wTExV-FLGpDXNJs1CbSyXcSdWUPBMvM,3959
+dcnum/segm/segm_torch/__init__.py,sha256=DtUqJTbj7ybrTbXlwHq1Y4SCzi22rMW9Cus6wX-iU-A,822
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+dcnum/segm/segm_torch/torch_preproc.py,sha256=kjabu76paw23kO7RP7Ik6IY60Kk1VBAHKBAedflA0aQ,4002
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+dcnum/write/writer.py,sha256=e6J8YVqhS7kzkpPIMoDMokJpqSy1WWNdOrwaJof1oVc,15601
+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,,

{dcnum-0.17.0.dist-info → dcnum-0.23.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: bdist_wheel (0.43.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

dcnum/feat/feat_moments/__init__.py

@@ -1,4 +0,0 @@
-# flake8: noqa: F401
-"""Feature computation: OpenCV moments-based features"""
-from .mt_legacy import moments_based_features
-

dcnum/segm/segmenter_gpu.py

@@ -1,64 +0,0 @@
-import abc
-from typing import Dict
-
-import numpy as np
-import scipy.ndimage as ndi
-
-
-from .segmenter import Segmenter
-
-
-class GPUSegmenter(Segmenter, abc.ABC):
-    hardware_processor = "gpu"
-    mask_postprocessing = False
-
-    def __init__(self,
-                 *,
-                 num_workers: int = None,
-                 kwargs_mask: Dict = None,
-                 debug: bool = False,
-                 **kwargs
-                 ):
-        """GPU base segmenter
-
-        Parameters
-        ----------
-        kwargs_mask: dict
-            Keyword arguments for mask post-processing (see `process_mask`)
-        debug: bool
-            Debugging parameters
-        kwargs:
-            Additional, optional keyword arguments for `segment_approach`
-            defined in the subclass.
-        """
-        if num_workers not in [None, 1]:
-            raise ValueError(f"Number of workers must not be larger than 1 "
-                             f"for GPU segmenter, got '{num_workers}'!")
-        super(GPUSegmenter, self).__init__(kwargs_mask=kwargs_mask,
-                                           debug=debug,
-                                           **kwargs)
-
-    def segment_batch(self,
-                      image_data: np.ndarray,
-                      start: int = None,
-                      stop: int = None):
-        if stop is None or start is None:
-            start = 0
-            stop = len(image_data)
-
-        image_slice = image_data[start:stop]
-        segm = self.segment_frame_wrapper()
-
-        labels = segm(image_slice)
-
-        # Make sure we have integer labels
-        if labels.dtype == bool:
-            new_labels = np.zeros_like(labels, dtype=np.uint16)
-            for ii in range(len(labels)):
-                ndi.label(
-                    input=labels[ii],
-                    output=new_labels[ii],
-                    structure=ndi.generate_binary_structure(2, 2))
-            labels = new_labels
-
-        return labels

dcnum-0.17.0.dist-info/RECORD

@@ -1,46 +0,0 @@
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-dcnum/segm/__init__.py,sha256=iiq_1A9DU5wMUcKnsZ53E7NyzCkbZCJeUDimzunE-OM,247
-dcnum/segm/segm_thresh.py,sha256=Z6buG3ia8uFJKTLE6BICM3n7Yw8IN-9f6_umIlx0xUk,1395
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