dcnum 0.13.3__py3-none-any.whl → 0.15.0__py3-none-any.whl

dcnum/meta/ppid.py

@@ -4,17 +4,38 @@ import collections
 import hashlib
 import inspect
 import pathlib
+from typing import Dict, List, Protocol
+import warnings
 
 
 #: Increment this string if there are breaking changes that make
 #: previous pipelines unreproducible.
-DCNUM_PPID_GENERATION = "5"
+DCNUM_PPID_GENERATION = "7"
 
 
-def compute_pipeline_hash(bg_id, seg_id, feat_id, gate_id,
-                          gen_id=DCNUM_PPID_GENERATION):
+class ClassWithPPIDCapabilities(Protocol):
+    def get_ppid(self) -> str:
+        """full pipeline identifier for the class (instance method)"""
+        pass
+
+    def get_ppid_code(self) -> str:
+        """string representing the class in the pipeline (classmethod)"""
+        pass
+
+    def get_ppid_from_ppkw(self) -> str:
+        """pipeline identifier from specific pipeline keywords (classmethod)"""
+        pass
+
+    def get_ppkw_from_ppid(self) -> Dict:
+        """class keywords from full pipeline identifier (staticmethod)"""
+        pass
+
+
+def compute_pipeline_hash(*, bg_id, seg_id, feat_id, gate_id,
+                          dat_id="unknown", gen_id=DCNUM_PPID_GENERATION):
     hasher = hashlib.md5()
-    hasher.update("|".join([gen_id, bg_id, seg_id, feat_id, gate_id]).encode())
+    hasher.update("|".join([
+        gen_id, dat_id, bg_id, seg_id, feat_id, gate_id]).encode())
     pph = hasher.hexdigest()
     return pph
 
@@ -37,7 +58,8 @@ def convert_to_dtype(value, dtype):
     return value
 
 
-def get_class_method_info(class_obj, static_kw_methods=None):
+def get_class_method_info(class_obj: ClassWithPPIDCapabilities,
+                          static_kw_methods: List = None):
     """Return dictionary of class info with static keyword methods docs
 
     Parameters
@@ -49,8 +71,14 @@ def get_class_method_info(class_obj, static_kw_methods=None):
         are extracted.
     """
     doc = class_obj.__doc__ or class_obj.__init__.__doc__
+    if hasattr(class_obj, "key"):
+        warnings.warn(f"{class_obj.__class__} implements `key` which is "
+                      f"deprecated. Please rename to `get_ppid_code`.",
+                      DeprecationWarning)
+        setattr(class_obj, "get_ppid_code", class_obj.key)
     info = {
-        "key": class_obj.key(),
+        "code": class_obj.get_ppid_code(),
+        "key": class_obj.get_ppid_code(),  # Deprecated
         "doc": doc,
         "title": doc.split("\n")[0],
         }
@@ -67,12 +95,25 @@ def get_class_method_info(class_obj, static_kw_methods=None):
     return info
 
 
-def kwargs_to_ppid(cls, method, kwargs):
+def kwargs_to_ppid(cls: ClassWithPPIDCapabilities,
+                   method: str,
+                   kwargs: Dict,
+                   allow_invalid_keys: bool = True):
     info = get_class_method_info(cls, [method])
 
     concat_strings = []
     if info["defaults"][method]:
         kwdefaults = info["defaults"][method]
+        kw_false = set(kwargs.keys()) - set(kwdefaults.keys())
+        if kw_false:
+            # This should not have happened.
+            msg = f"Invalid kwargs {kw_false} specified for method " \
+                  f"'{method}'! Valid kwargs are {sorted(kwdefaults.keys())}."
+            if allow_invalid_keys:
+                warnings.warn(msg + " Please cleanup your code!",
+                              DeprecationWarning)
+            else:
+                raise KeyError(msg)
         kwannot = info["annotations"][method]
         kws = list(kwdefaults.keys())
         kws_abrv = get_unique_prefix(kws)

dcnum/read/hdf5_data.py

@@ -169,6 +169,11 @@ class HDF5Data:
                     and (self.pixel_size < 0.255 or self.pixel_size > 0.275)):
                 warnings.warn(
                     f"Correcting for invalid pixel size in '{self.path}'!")
+                warnings.warn(
+                    "Correcting the pixel size is deprecated in dcnum. Please "
+                    "make sure your input data are clean before processing.",
+                    DeprecationWarning
+                )
                 # Set default pixel size for Rivercyte devices
                 self.pixel_size = 0.2645
 
@@ -221,7 +226,10 @@ class HDF5Data:
         return self.meta.get("imaging:pixel size", 0)
 
     @pixel_size.setter
-    def pixel_size(self, pixel_size):
+    def pixel_size(self, pixel_size: float):
+        # Reduce pixel_size accuracy to 8 digits after the point to
+        # enforce pipeline reproducibility (see get_ppid_from_ppkw).
+        pixel_size = float(f"{pixel_size:.8f}")
         self.meta["imaging:pixel size"] = pixel_size
 
     @property
@@ -234,7 +242,7 @@ class HDF5Data:
         """
         if self._feats is None:
             feats = []
-            for feat in self.h5["events"]:
+            for feat in self.keys():
                 if feat in PROTECTED_FEATURES:
                     feats.append(feat)
             self._feats = feats
@@ -249,6 +257,33 @@ class HDF5Data:
         self._basin_data.clear()
         self.h5.close()
 
+    def get_ppid(self):
+        return self.get_ppid_from_ppkw({"pixel_size": self.pixel_size})
+
+    @classmethod
+    def get_ppid_code(cls):
+        return "hdf"
+
+    @classmethod
+    def get_ppid_from_ppkw(cls, kwargs):
+        # Data does not really fit into the PPID scheme we use for the rest
+        # of the pipeline. This implementation here is custom.
+        code = cls.get_ppid_code()
+        kwid = f"p={kwargs['pixel_size']:.8f}".rstrip("0")
+        return ":".join([code, kwid])
+
+    @staticmethod
+    def get_ppkw_from_ppid(dat_ppid):
+        # Data does not fit in the PPID scheme we use, but we still
+        # would like to pass pixel_size to __init__ if we need it.
+        code, pp_dat_kwargs = dat_ppid.split(":")
+        if code != HDF5Data.get_ppid_code():
+            raise ValueError(f"Could not find data method '{code}'!")
+        p, val = pp_dat_kwargs.split("=")
+        if p != "p":
+            raise ValueError(f"Invalid parameter '{p}'!")
+        return {"pixel_size": float(val)}
+
     def get_basin_data(self, index):
         """Return HDF5Data info for a basin index in `self.basins`
 
@@ -280,6 +315,16 @@ class HDF5Data:
                 h5dat = HDF5Data(path)
                 features = bn_dict.get("features")
                 if features is None:
+                    # Only get the features from the actual HDF5 file.
+                    # If this file has basins as well, the basin metadata
+                    # should have been copied over to the parent file. This
+                    # makes things a little cleaner, because basins are not
+                    # nested, but all basins are available in the top file.
+                    # See :func:`write.store_metadata` for copying metadata
+                    # between files.
+                    # The writer can still specify "features" in the basin
+                    # metadata, then these basins are indeed nested, and
+                    # we consider that ok as well.
                     features = sorted(h5dat.h5["events"].keys())
                 self._basin_data[index] = (h5dat, features)
         return self._basin_data[index]

dcnum/segm/__init__.py

@@ -1,18 +1,6 @@
 # flake8: noqa: F401
-import functools
-
-from .segmenter import Segmenter
+from .segmenter import Segmenter, get_available_segmenters
 from .segmenter_cpu import CPUSegmenter
 from .segmenter_gpu import GPUSegmenter
 from .segmenter_manager_thread import SegmenterManagerThread
 from . import segm_thresh
-
-
-@functools.cache
-def get_available_segmenters():
-    """Return dictionary of available segmenters"""
-    segmenters = {}
-    for scls in Segmenter.__subclasses__():
-        for cls in scls.__subclasses__():
-            segmenters[cls.key()] = cls
-    return segmenters

dcnum/segm/segm_thresh.py

@@ -8,6 +8,7 @@ class SegmentThresh(CPUSegmenter):
         "fill_holes": True,
         "closing_disk": 2,
     }
+    requires_background_correction = True
 
     def __init__(self, thresh=-6, *args, **kwargs):
         """Simple image thresholding segmentation

dcnum/segm/segmenter.py

@@ -1,17 +1,21 @@
 import abc
+import copy
 import functools
 import inspect
 import logging
+import warnings
 
 import cv2
 import numpy as np
 import scipy.ndimage as ndi
 from skimage import morphology
 
-from ..meta.ppid import kwargs_to_ppid
+from ..meta.ppid import kwargs_to_ppid, ppid_to_kwargs
 
 
 class Segmenter(abc.ABC):
+    #: Required hardware ("cpu" or "gpu") defined in first-level subclass.
+    hardware_processor = "none"
     #: Whether to enable mask post-processing. If disabled, you should
     #: make sure that your mask is properly defined and cleaned or you
     #: have to call `process_mask` in your `segment_approach` implementation.
@@ -55,13 +59,11 @@ class Segmenter(abc.ABC):
                 "`kwargs_mask` has been specified, but mask post-processing "
                 f"is disabled for segmenter {self.__class__}")
 
-    @classmethod
-    def key(cls):
-        """The unique key/name of this segmenter class"""
-        key = cls.__name__.lower()
-        if key.startswith("segment"):
-            key = key[7:]
-        return key
+    @staticmethod
+    @functools.cache
+    def get_disk(radius):
+        """Cached `skimage.morphology.disk(radius)`"""
+        return morphology.disk(radius)
 
     def get_ppid(self):
         """Return a unique segmentation pipeline identifier
@@ -85,36 +87,58 @@ class Segmenter(abc.ABC):
 
         KW_MASK represents keyword arguments for `process_mask`.
         """
-        return self.get_ppid_from_kwargs(self.kwargs, self.kwargs_mask)
+        return self.get_ppid_from_ppkw(self.kwargs, self.kwargs_mask)
+
+    @classmethod
+    def get_ppid_code(cls):
+        """The unique code/name of this segmenter class"""
+        code = cls.__name__.lower()
+        if code.startswith("segment"):
+            code = code[7:]
+        return code
 
     @classmethod
-    def get_ppid_from_kwargs(cls, kwargs, kwargs_mask=None):
+    def get_ppid_from_ppkw(cls, kwargs, kwargs_mask=None):
         """Return the pipeline ID from given keyword arguments
 
         See Also
         --------
         get_ppid: Same method for class instances
         """
+        kwargs = copy.deepcopy(kwargs)
         if kwargs_mask is None and kwargs.get("kwargs_mask", None) is None:
             raise KeyError("`kwargs_mask` must be either specified as "
                            "keyword argument to this method or as a key "
                            "in `kwargs`!")
         if kwargs_mask is None:
             # see check above (kwargs_mask may also be {})
-            kwargs_mask = kwargs["kwargs_mask"]
+            kwargs_mask = kwargs.pop("kwargs_mask")
         # Start with the default mask kwargs defined for this subclass
-        kwargs_mask_used = cls.mask_default_kwargs
+        kwargs_mask_used = copy.deepcopy(cls.mask_default_kwargs)
         kwargs_mask_used.update(kwargs_mask)
-        key = cls.key()
+        key = cls.get_ppid_code()
         csegm = kwargs_to_ppid(cls, "segment_approach", kwargs)
         cmask = kwargs_to_ppid(cls, "process_mask", kwargs_mask_used)
         return ":".join([key, csegm, cmask])
 
     @staticmethod
-    @functools.cache
-    def get_disk(radius):
-        """Cached `skimage.morphology.disk(radius)`"""
-        return morphology.disk(radius)
+    def get_ppkw_from_ppid(segm_ppid):
+        """Return keyword arguments for this pipeline identifier"""
+        code, pp_kwargs, pp_kwargs_mask = segm_ppid.split(":")
+        for cls_code in get_available_segmenters():
+            if cls_code == code:
+                cls = get_available_segmenters()[cls_code]
+                break
+        else:
+            raise ValueError(
+                f"Could not find segmenter '{code}'!")
+        kwargs = ppid_to_kwargs(cls=cls,
+                                method="segment_approach",
+                                ppid=pp_kwargs)
+        kwargs["kwargs_mask"] = ppid_to_kwargs(cls=cls,
+                                               method="process_mask",
+                                               ppid=pp_kwargs_mask)
+        return kwargs
 
     @staticmethod
     def process_mask(labels, *,
@@ -240,3 +264,20 @@ class Segmenter(abc.ABC):
     @abc.abstractmethod
     def segment_batch(self, data, start=None, stop=None):
         """Return the integer labels for an entire batch"""
+
+    @classmethod
+    def get_ppid_from_kwargs(cls, *args, **kwargs):
+        warnings.warn(
+            "Please use get_ppid_from_ppkw instead of get_ppid_from_kwargs.",
+            DeprecationWarning)
+        return cls.get_ppid_from_ppkw(*args, **kwargs)
+
+
+@functools.cache
+def get_available_segmenters():
+    """Return dictionary of available segmenters"""
+    segmenters = {}
+    for scls in Segmenter.__subclasses__():
+        for cls in scls.__subclasses__():
+            segmenters[cls.get_ppid_code()] = cls
+    return segmenters

dcnum/segm/segmenter_cpu.py

@@ -14,6 +14,8 @@ mp_spawn = mp.get_context('spawn')
 
 
 class CPUSegmenter(Segmenter, abc.ABC):
+    hardware_processor = "cpu"
+
     def __init__(self, num_workers=None, *args, **kwargs):
         super(CPUSegmenter, self).__init__(*args, **kwargs)
         self.num_workers = num_workers or mp.cpu_count()

dcnum/segm/segmenter_gpu.py

@@ -9,6 +9,7 @@ from .segmenter import Segmenter
 
 
 class GPUSegmenter(Segmenter, abc.ABC):
+    hardware_processor = "gpu"
     mask_postprocessing = False
 
     def __init__(self, *args, **kwargs):

dcnum/write/deque_writer_thread.py

@@ -19,7 +19,7 @@ class DequeWriterThread(threading.Thread):
         ----------
         path_out:
             Path to the output HDF5 file
-        dq:
+        dq: collections.deque
             `collections.deque` object from which data are taken
             using `popleft()`.
         """

dcnum/write/writer.py

@@ -2,6 +2,7 @@ import hashlib
 import json
 import pathlib
 from typing import List
+import warnings
 
 import h5py
 import hdf5plugin
@@ -10,6 +11,11 @@ import numpy as np
 from .._version import version
 
 
+class CreatingFileWithoutBasinWarning(UserWarning):
+    """Issued when creating a basin-based dataset without basins"""
+    pass
+
+
 class HDF5Writer:
     def __init__(self, path, mode="a", ds_kwds=None):
         """Write deformability cytometry HDF5 data"""
@@ -136,6 +142,33 @@ class HDF5Writer:
         ds.resize(offset + dsize, axis=0)
         ds[offset:offset + dsize] = data
 
+    def store_log(self,
+                  log: str,
+                  data: List[str],
+                  override: bool = False):
+        """Store log data
+
+        Store the log data under the key `log`. The `data`
+        kwarg must be a list of strings. If the log entry
+        already exists, `ValueError` is raised unless
+        `override` is set to True.
+        """
+        logs = self.h5.require_group("logs")
+        if log in logs:
+            if override:
+                del logs[log]
+            else:
+                raise ValueError(
+                    f"Log '{log}' already exists in {self.h5.filename}!")
+        logs.create_dataset(
+            name=log,
+            data=data,
+            shape=(len(data),),
+            # maximum line length
+            dtype=f"S{max([len(ll) for ll in data])}",
+            chunks=True,
+            **self.ds_kwds)
+
 
 def create_with_basins(
         path_out: str | pathlib.Path,
@@ -154,6 +187,10 @@ def create_with_basins(
         commonly used for relative and absolute paths).
     """
     path_out = pathlib.Path(path_out)
+    if not basin_paths:
+        warnings.warn(f"Creating basin-based file '{path_out}' without any "
+                      f"basins, since the list `basin_paths' is empty!",
+                      CreatingFileWithoutBasinWarning)
     with HDF5Writer(path_out, mode="w") as hw:
         # Get the metadata from the first available basin path
 
@@ -184,7 +221,7 @@ def create_with_basins(
             # Copy the metadata from the representative path.
             if prep is not None:
                 # copy metadata
-                with h5py.File(prep) as h5:
+                with h5py.File(prep, libver="latest") as h5:
                     copy_metadata(h5_src=h5, h5_dst=hw.h5)
                     # extract features
                     features = sorted(h5["events"].keys())
@@ -202,13 +239,14 @@ def create_with_basins(
 
 
 def copy_metadata(h5_src: h5py.File,
-                  h5_dst: h5py.File):
+                  h5_dst: h5py.File,
+                  copy_basins=True):
     """Copy attributes, tables, logs, and basins from one H5File to another
 
     Notes
     -----
     Metadata in `h5_dst` are never overridden, only metadata that
-    are not defined are added.
+    are not defined already are added.
     """
     # compress data
     ds_kwds = {}
@@ -219,8 +257,11 @@ def copy_metadata(h5_src: h5py.File,
     src_attrs = dict(h5_src.attrs)
     for kk in src_attrs:
         h5_dst.attrs.setdefault(kk, src_attrs[kk])
+    copy_data = ["logs", "tables"]
+    if copy_basins:
+        copy_data.append("basins")
     # copy other metadata
-    for topic in ["basins", "logs", "tables"]:
+    for topic in copy_data:
         if topic in h5_src:
             for key in h5_src[topic]:
                 h5_dst.require_group(topic)

{dcnum-0.13.3.dist-info → dcnum-0.15.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.13.3
+Version: 0.15.0
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

dcnum-0.15.0.dist-info/RECORD

@@ -0,0 +1,43 @@
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+dcnum/_version.py,sha256=oHv-EAjiXbJma3jZ0Tq6UPimiWYyyw2Ao9S8zdq9uWs,413
+dcnum/feat/__init__.py,sha256=JqlgzOgDJhoTk8WVYcIiKTWq9EAM16_jGivzOtN6JGo,325
+dcnum/feat/event_extractor_manager_thread.py,sha256=V2idRAlC7bdsA8I40RAUkqz3jtWmTeb4cjPXpRjr8Ik,6145
+dcnum/feat/gate.py,sha256=srobj5p2RDr_S2SUtbwGbTKatnc_aPSndt0cR2P9zoY,7060
+dcnum/feat/queue_event_extractor.py,sha256=RYz0VNtV8OVGDFn9MrYWM5NaB4rXLiJch9MTKDnccs0,14453
+dcnum/feat/feat_background/__init__.py,sha256=nIKAGKBFYlLvm8UdkEzBB6V_FC_lhxo3xG-u-p2y3es,305
+dcnum/feat/feat_background/base.py,sha256=N1SL5NCZ7gTS5AQONxEH31PFJBx0zvVjCaA4mprheuY,7974
+dcnum/feat/feat_background/bg_roll_median.py,sha256=E86AiSzpw0RZ0nYL4UdKKkskS5ywKJCLeHlWYfTPS0k,12781
+dcnum/feat/feat_background/bg_sparse_median.py,sha256=COJeY8suHmrHBWiXxTLw3C17-QOnc4R75GMdZiuU3cc,17670
+dcnum/feat/feat_brightness/__init__.py,sha256=o6AebVlmydwNgVF5kW6ITqJyFreoKrU3Ki_3EC8If-s,155
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+dcnum/feat/feat_moments/ct_opencv.py,sha256=_qyHCGvylVxruMWafvVbVOzhWGXLoFi10LReNxGcWhY,463
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+dcnum-0.15.0.dist-info/LICENSE,sha256=YRChA1C8A2E-amJbudwMcbTCZy_HzmeY0hMIvduh1MM,1089
+dcnum-0.15.0.dist-info/METADATA,sha256=ITzdZGcaKxRw_llMIvman5gh8uOuJ7Ryn2W9raEMy1E,2172
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+dcnum-0.15.0.dist-info/top_level.txt,sha256=Hmh38rgG_MFTVDpUDGuO2HWTSq80P585Het4COQzFTg,6
+dcnum-0.15.0.dist-info/RECORD,,

{dcnum-0.13.3.dist-info → dcnum-0.15.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.3)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

dcnum-0.13.3.dist-info/RECORD

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