dclab 0.62.7__cp38-cp38-macosx_11_0_arm64.whl → 2.18.0__cp38-cp38-macosx_11_0_arm64.whl

dclab/rtdc_dataset/fmt_hierarchy/events.py

@@ -3,7 +3,6 @@ import warnings
 
 import numpy as np
 
-from ...util import copy_if_needed
 from .mapper import map_indices_child2parent
 
 
@@ -38,7 +37,7 @@ class ChildNDArray(ChildBase):
         super(ChildNDArray, self).__init__(child)
         self.feat = feat
 
-    def __array__(self, dtype=None, copy=copy_if_needed, *args, **kwargs):
+    def __array__(self, dtype=None, copy=False, *args, **kwargs):
         warnings.warn("Please avoid calling the `__array__` method of the "
                       "`ChildNDArray`. It may consume a lot of memory. "
                       "Consider using a generator instead.",
@@ -70,7 +69,7 @@ class ChildScalar(np.lib.mixins.NDArrayOperatorsMixin):
         self._ufunc_attrs = {}
         self.ndim = 1  # matplotlib might expect this from an array
 
-    def __array__(self, dtype=None, copy=copy_if_needed, *args, **kwargs):
+    def __array__(self, dtype=None, copy=False, *args, **kwargs):
         if self._array is None:
             hparent = self.child.hparent
             filt_arr = hparent.filter.all
@@ -122,7 +121,7 @@ class ChildTraceItem(ChildBase):
         super(ChildTraceItem, self).__init__(child)
         self.flname = flname
 
-    def __array__(self, dtype=None, copy=copy_if_needed, *args, **kwargs):
+    def __array__(self, dtype=None, copy=False, *args, **kwargs):
         warnings.warn("Please avoid calling the `__array__` method of the "
                       "`ChildTraceItem`. It may consume a lot of memory. "
                       "Consider using a generator instead.",

dclab/rtdc_dataset/linker.py

@@ -0,0 +1,124 @@
+"""Tools for linking HDF5 datasets across files"""
+from __future__ import annotations
+
+import io
+import pathlib
+from typing import BinaryIO, Literal
+
+import h5py
+
+
+class ExternalDataForbiddenError(BaseException):
+    """Raised when a dataset contains external data
+
+    External data are a security risk, because they could be
+    used to access data that are not supposed to be accessed.
+    This is especially critical when the data are accessed within
+    a web server process (e.g. in DCOR).
+    """
+    pass
+
+
+def assert_no_external(h5):
+    """Raise ExternalDataForbiddenError if `h5` refers to external data"""
+    has_ext, path_ext = check_external(h5)
+    if has_ext:
+        raise ExternalDataForbiddenError(
+            f"Dataset {h5.file.filename} contains external data, but these "
+            f"are not permitted for security reasons ({path_ext})!")
+
+
+def check_external(h5):
+    """Check recursively, whether an h5py object contains external data
+
+    External data includes binary data in external files, virtual
+    datasets, and external links.
+
+    Returns a tuple of either
+
+    - `(True, path_ext)` if the object contains external data
+    - `(False, None)` if this is not the case
+
+    where `path_ext` is the path to the group or dataset in `h5`.
+
+    .. versionadded:: 0.51.0
+
+    """
+    for key in h5:
+        obj = h5[key]
+        if (obj.file != h5.file  # not in same file
+                or (isinstance(obj, h5py.Dataset)
+                    and (obj.is_virtual  # virtual dataset
+                         or obj.external))):  # external dataset
+            # These are external data
+            return True, f"{h5.name}/{key}".replace("//", "/")
+        elif isinstance(obj, h5py.Group):
+            # Perform recursive check for external data
+            has_ext, path_ext = check_external(obj)
+            if has_ext:
+                return True, path_ext
+    else:
+        return False, None
+
+
+def combine_h5files(
+        paths: list,
+        external: Literal["follow", "raise"] = "follow"
+        ) -> BinaryIO:
+    """Create an in-memory file that combines multiple .rtdc files
+
+    The .rtdc files must have the same number of events. The in-memory
+    file is populated with the "events" data from `paths` according to
+    the order that `paths` are given in. Metadata, including logs, basins,
+    and tables are only taken from the first path.
+
+    .. versionadded:: 0.51.0
+
+    Parameters
+    ----------
+    paths: list of str or pathlib.Path
+        Paths of the input .rtdc files. The first input file is always
+        used as a source for the metadata. The other files only complement
+        the features.
+    external: str
+        Defines how external (links, binary, virtual) data in `paths`
+        should be handled. The default is to "follow" external datasets or
+        links to external data. In a zero-trust context, you can set this
+        to "raise" which will cause an :class:`.ExternalDataForbiddenError`
+        exception when external data are encountered.
+
+    Returns
+    -------
+    fd: BinaryIO
+        seekable, file-like object representing an HDF5 file opened in
+        binary mode; This can be passed to `:class:h5py.File`
+    """
+    fd = io.BytesIO()
+    with h5py.File(fd, "w", libver="latest") as hv:
+        for ii, pp in enumerate(paths):
+            pp = pathlib.Path(pp).resolve()
+            with h5py.File(pp, libver="latest") as h5:
+                if external == "raise":
+                    # Check for external data
+                    assert_no_external(h5)
+                if ii == 0:
+                    # Only write attributes once.
+                    # Interestingly, writing the attributes takes
+                    # the most time. Maybe there is some shortcut
+                    # that can be taken (since e.g. we know we don't have to
+                    # check for existing attributes).
+                    # https://github.com/h5py/h5py/blob/master/
+                    # h5py/_hl/attrs.py
+                    hv.attrs.update(h5.attrs)
+                    # Also, write basins/logs/tables/... (anything that is
+                    # not events) only once.
+                    for group in h5:
+                        if group != "events":
+                            hv[group] = h5py.ExternalLink(str(pp), group)
+                # Append features
+                hve = hv.require_group("events")
+                for feat in h5["events"]:
+                    if feat not in hve:
+                        hve[feat] = h5py.ExternalLink(str(pp),
+                                                      f"/events/{feat}")
+    return fd

dclab/util.py

@@ -10,12 +10,6 @@ import numpy as np
 from .rtdc_dataset.config import Configuration, ConfigurationDict
 
 
-if np.lib.NumpyVersion(np.__version__) >= "2.0.0":
-    copy_if_needed = None
-else:
-    copy_if_needed = False
-
-
 class file_monitoring_lru_cache:
     """Decorator for caching data extracted from files
 

{dclab-0.62.7.dist-info → dclab-2.18.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dclab
-Version: 0.62.7
+Version: 2.18.0
 Summary: Library for real-time deformability cytometry (RT-DC)
 Author: Benedikt Hartmann, Eoghan O'Connell, Maik Herbig, Maximilian Schlögel, Nadia Sbaa, Paul Müller, Philipp Rosendahl, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>
@@ -23,7 +23,7 @@ Requires-Dist: importlib-resources>=6.0
 Requires-Dist: numpy<3,>=1.21
 Requires-Dist: scipy<2,>=1.10.0
 Provides-Extra: all
-Requires-Dist: dclab[dcor,export,http,s3,tdms]; extra == "all"
+Requires-Dist: dclab[dcor,export,http,lme4,s3,tdms]; extra == "all"
 Provides-Extra: dcor
 Requires-Dist: requests<3,>=2.31.0; extra == "dcor"
 Provides-Extra: export
@@ -31,6 +31,8 @@ Requires-Dist: fcswrite>=0.5.0; extra == "export"
 Requires-Dist: imageio[ffmpeg]; extra == "export"
 Provides-Extra: http
 Requires-Dist: requests<3,>=2.31.0; extra == "http"
+Provides-Extra: lme4
+Requires-Dist: rpy2>=2.9.4; extra == "lme4"
 Provides-Extra: s3
 Requires-Dist: boto3>=1.34.31; extra == "s3"
 Provides-Extra: tdms

{dclab-0.62.7.dist-info → dclab-2.18.0.dist-info}/RECORD

@@ -1,15 +1,15 @@
 dclab/kde_methods.py,sha256=awlqkj819VRJzArG6Fx6myDa6qGpLoZ8S9IJ1J1YECA,9206
-dclab/_version.py,sha256=2nNmtDl49w2uonQ4lw3PC68spDp8sFy-2CvnHEXJVdc,413
-dclab/util.py,sha256=nLL5jwG14h1YFJ_d0L-5DwsWgyfst5hVndaiLbTkYH4,5253
+dclab/_version.py,sha256=QyMxKDzFsqXDA7bVrQozJznaASbsECKe57aBBNAljsA,413
+dclab/util.py,sha256=FcRsWcyKkKkfX2nZCShjJ5wPccr7U7NHsIDd_WEws6w,5141
 dclab/downsampling.pyx,sha256=OK7zbgGLl5gVyoU8ZBHo9EWwb8C9ChavmLNEvQvC9T0,7258
 dclab/__init__.py,sha256=1mskJAUo8HbvDhJRJFbcFB6HccFeqoRUCEHLuS64t_g,812
 dclab/warn.py,sha256=MjJvyQeuvIXFQ2-fHDzbmXJ0scnHqqRJlIxfuLI_utE,523
 dclab/cached.py,sha256=eWTYBiI-HQM7JuPH-oxa5LLnhAX32GpRwlYg2kQ3sTA,2917
-dclab/http_utils.py,sha256=YtZHEwB-BBBo2fCvwhlJvlnWvfWFMHclqol3OIJ7atM,10910
+dclab/http_utils.py,sha256=TGqgiaUV-Z6Wiae__Yze-uHRWX57846ZnlV10ajzv2E,10562
 dclab/polygon_filter.py,sha256=qexmo-rXe06CUPZhN6EMJy4y4B5gXZeqejdvIB2arOE,13480
 dclab/statistics.py,sha256=tJDqPlY_Jw2Hhl-s7ugMBSZAxcRuPu4LQuBAZBXz7t8,6355
 dclab/kde_contours.py,sha256=5K7PzZz-FtSGvW4IR2tLpbEKKqCSsSTQPsupu7zIsPg,6745
-dclab/downsampling.cpython-38-darwin.so,sha256=rjbxMCNBQJnOREt1pCRMFQIo3KFrLEpH91zdnu8pvYg,258320
+dclab/downsampling.cpython-38-darwin.so,sha256=FNBTHufTLyFBtuL_RcuBYIDu_70hVQc0tp02o2mKADM,258320
 dclab/isoelastics/iso_LE-2D-FEM-19-volume-deform.txt,sha256=vTcazOlOXo3BQ0NQtGB_IdHKA0neOLXZ_d3JuMU--RE,83358
 dclab/isoelastics/iso_HE-3D-FEM-22-area_um-deform.txt,sha256=IjULG1KO-hClaYPoJJnwPbF2TkS9i9jxF1tbhhQTClY,71350
 dclab/isoelastics/iso_HE-2D-FEM-22-volume-deform.txt,sha256=aLOWxev_hvyP2yWquomcogn3Ze4SBfvqz-qmTOOibNw,97512
@@ -34,10 +34,10 @@ dclab/features/emodulus/scale_linear.py,sha256=5tZfOpG4QSSEMlwSoA_3XRQuY0tiZ3CSm
 dclab/features/emodulus/lut_HE-3D-FEM-22.txt,sha256=1Sg4ys0ykT7Q_jFM28XS0uJ85nZd_ha7BDXdN2rsPIA,47248
 dclab/features/emodulus/load.py,sha256=Q9rII-7Om-f0m183VNeJUxNno7at1reigKtbzdrWgjE,8557
 dclab/features/emodulus/viscosity.py,sha256=aBm1pQa9cFAOBnO07UWMj87bw6fQpmW1IlWWD0MEtgw,9438
-dclab/lme4/lme4_template.R,sha256=CEXQIquvYCla9dCvRYgiBemI6fiVgAKnJTetJA2LAtk,2570
-dclab/lme4/__init__.py,sha256=5WPFMTK-Yia3NJuwZEEBQ3fCyW3DiFgpZFrAwU33TV4,272
-dclab/lme4/rsetup.py,sha256=kH9VFtcK83ZaF9jvh1n5kcmGmPLLsmCPia_ElEHBLes,5890
-dclab/lme4/wrapr.py,sha256=rdIc2hS8GhgdU9WFA6pLzohJGlBga-mkm60qqqk6VO4,15017
+dclab/lme4/__init__.py,sha256=Y_oqYEqNnHCjxfdzkoP0ZXPCQx6XSKqwt1pAgdGF2dA,235
+dclab/lme4/rsetup.py,sha256=siVWXt0niXAqD20d2quOjVzaZc4-zF0i81G_HRZE6q0,6951
+dclab/lme4/wrapr.py,sha256=MzJDUZ7L_5xDWVtl5vrDgTJoum2vrxfP0dYwPMcHIPY,16977
+dclab/lme4/rlibs.py,sha256=3oHSrSykeQB9ldvrV4Ite9EffIURUwCo3bn4uBpVeSk,2539
 dclab/cli/task_tdms2rtdc.py,sha256=u0L1Fq9rXIeQG9b72SuUIh_qYC6fG2xXxht9_rcdCao,8283
 dclab/cli/__init__.py,sha256=84YzzV6aE_NY-o7wvqgvUoxBLvIOEXpSUbkVcGRyzQ0,483
 dclab/cli/task_condense.py,sha256=uNZzm04VuQOXJi6uXPmaLdQCk0g8ONueiO4p67yJv0k,8546
@@ -64,49 +64,50 @@ dclab/external/skimage/measure.py,sha256=y1idCqD9TUxp3-QnOiWR_d674OKaeqBJ4MN2-gV
 dclab/external/skimage/LICENSE,sha256=ivsSBvn3c0R9mOctWRRdza7C7wdZSRYgCVxlVqUdlB8,1452
 dclab/external/skimage/pnpoly.py,sha256=r8hFNiTz5XlUoNZjosqA0iyv1FPn0l7ewbplgFgkdaw,1347
 dclab/external/skimage/_find_contours.py,sha256=16v5eeTZBmevG8SSuXtJ6yUpVPhwfSmtc8pDD0nuuOU,9340
-dclab/external/skimage/_find_contours_cy.cpython-38-darwin.so,sha256=E35HOyc5GlqeJAsQy8nYJ0FaHywFTyRFrtW0USc-EzA,204152
+dclab/external/skimage/_find_contours_cy.cpython-38-darwin.so,sha256=rQkLcGaS1k3RLfghHe198naX1tHtHoes8dcY_JP5CAA,204152
 dclab/external/skimage/__init__.py,sha256=-B2QUKHAFzQuBWuuKvPDC5JIl0Zb-x3OGmbwPaE9VwQ,72
 dclab/external/skimage/_pnpoly.pyx,sha256=Qdn6xPazDschBqbr46DzB75MB2MnqvdnoTSBMK7kUGE,2504
-dclab/external/skimage/_pnpoly.cpython-38-darwin.so,sha256=SW95Jc6iyApjbTVdUvJiT39BZiPlnYIAwkQcybHH_5Q,221776
+dclab/external/skimage/_pnpoly.cpython-38-darwin.so,sha256=LbbcT_nPTzO6gezZbDlyZmfbRbD9g636GyQnmqEEqYY,221776
 dclab/external/skimage/_find_contours_cy.pyx,sha256=pZJOBhMHzYEMkcz4WQVyjn7jDNrdjCfet47FU1hRAxk,7161
 dclab/external/skimage/_shared/geometry.pxd,sha256=kRsu9ifv_rL3kbRIgSLf86p0hn2oTMp6s013lZ9bBZM,346
-dclab/external/skimage/_shared/geometry.cpython-38-darwin.so,sha256=cQp0xWCPe-mYRFNCQmMKTkwhXaoRgKuyxj13GhdnB7c,55872
+dclab/external/skimage/_shared/geometry.cpython-38-darwin.so,sha256=4OA-BITBrYlTkK-6kgxdrvJcOVgVrNumGxOxyJvBIkY,55872
 dclab/external/skimage/_shared/__init__.py,sha256=2sHZwTtJSlMTa3Q2YSvQW7jrPLMUSqDJQa-ROe5zfcw,37
 dclab/external/skimage/_shared/geometry.pyx,sha256=miCHUh6mBDbRRIoaF_0xAER1MRzsCAzFdlYQZhV7RmE,1667
 dclab/definitions/feat_logic.py,sha256=SXsSlAusgtE3uXcPu84dQwYZ07zxmV37DmPednA3_dM,5823
 dclab/definitions/meta_parse.py,sha256=YdaTdM8DAMsIFn5ITH9OHYGTXeAOBGWtx22oVjxXcWk,2393
 dclab/definitions/__init__.py,sha256=56VL7rNTjP61gpGgN2GEUKicds2aBz_nWNwzfNxO_l8,2781
-dclab/definitions/meta_const.py,sha256=zqE-SrD2tJMCFWdtp_IenwnbIQg0lulvbQAw9dK0Gho,13125
+dclab/definitions/meta_const.py,sha256=Nci-QFl6cxe2p8tvfGVIWsRO8NArFOyiA2jPFUIY23M,12399
 dclab/definitions/feat_const.py,sha256=3zii5bXN0d0lMtkiI8dR9ivNlNQYosZASAlOg1UKKPA,9634
 dclab/definitions/meta_logic.py,sha256=wCgb7DPRHaR8DCWw_VbwNkpslUnazzWfgX0iS8oEe90,4194
 dclab/rtdc_dataset/config.py,sha256=MvBteFya3R6Ch3U6UgTakCsJoBgVykTxS_Z25STWPHU,17432
-dclab/rtdc_dataset/check.py,sha256=lJNaz4QTe2WNlxik6zSohRHTiAYuP_bKOzSDjPGTUS0,35006
-dclab/rtdc_dataset/feat_basin.py,sha256=3ev_a31Sa17oL_vK_ziP7_yrGxZpx0bofpkTrH2O7xU,20700
+dclab/rtdc_dataset/check.py,sha256=6l9E2amboqgU9go1BaPtOJgeDgl4GSUuGteF1B2M2X8,32406
+dclab/rtdc_dataset/feat_basin.py,sha256=nxcFjhQiFqsdW0wucEjOMyvZFjCNdS7fFFVrvKvI0EE,19997
 dclab/rtdc_dataset/fmt_s3.py,sha256=OavOOGa2oOyG-VSfehFf6JVNs2k5iZalRm6ZTBu6sY4,10642
 dclab/rtdc_dataset/feat_temp.py,sha256=XbDIS1iUUkRH0Zp9uVlwvK_untJ7hkOnKshK1Drsnt8,3694
 dclab/rtdc_dataset/__init__.py,sha256=MUHSGVQJ4Zc0IyU2lf01dpDWyOyNveHip-UjSkmPNvQ,486
 dclab/rtdc_dataset/core.py,sha256=DEaN6-w0she-ylE6ZuNRLmB4Q77fiv7xC01IzUTz-jk,37672
 dclab/rtdc_dataset/export.py,sha256=OxixysUUAlAoOnqip_GtkDSeLPenMQVNeO8zDipxjgo,29484
 dclab/rtdc_dataset/fmt_dict.py,sha256=gumVQOiVVDFUKow_483PY7cxInqo-NiBBnBhIU8s4lg,3009
+dclab/rtdc_dataset/linker.py,sha256=vp2yaqcbb5LESu8MO9WG9--NJor2MWkNcCfoAvlEKq0,4629
 dclab/rtdc_dataset/writer.py,sha256=tOL-Hn9qC9bhJgJvQQgE8sTwS3DV5IB1mCd1M79qK7o,40427
 dclab/rtdc_dataset/filter.py,sha256=AFPUBzOIi3pqXgUdMQ5CIi9ZeGOKC71rfSZKLMLgtog,10023
 dclab/rtdc_dataset/fmt_http.py,sha256=vXVxRLXZp2_V1v3xk4lu4VUHYXfNHJdsRkVt3trC1RU,3374
 dclab/rtdc_dataset/load.py,sha256=wGJuIv7pH1zpBhg6Cj_H0wxHZb-KwHR8TWnyDosCBBA,2473
-dclab/rtdc_dataset/copier.py,sha256=ENh7PQ1fjUcW6WtcIhyjOi3Hn1-1PA2navwrFqRHB6M,13998
+dclab/rtdc_dataset/copier.py,sha256=8xSogZ73SU7y2HaTRY1zCml5Q8pZSJsDLiUozCDzwfY,11990
 dclab/rtdc_dataset/feat_anc_plugin/__init__.py,sha256=Em8nKxzex6M46Q86pRoSdrzb02XBiTY9u-npODvwrwk,119
 dclab/rtdc_dataset/feat_anc_plugin/plugin_feature.py,sha256=ED7vAtHgMXoanbeoUdklDAocj0Pq_cpckmCJ-YWqwr8,12381
-dclab/rtdc_dataset/fmt_hierarchy/events.py,sha256=pRqiFJpBoTwL2krG3asmLw4Fyp7O-vZDzbUIBpWx7QQ,4547
+dclab/rtdc_dataset/fmt_hierarchy/events.py,sha256=tr4S0_chhQidxWmcTook6fXJNtmtfdFfhkTjtl4rwV4,4485
 dclab/rtdc_dataset/fmt_hierarchy/mapper.py,sha256=dgGLO1ki2upV9QP6h7DCyNGgcMw45bzFbXc1CyyFAGw,4210
 dclab/rtdc_dataset/fmt_hierarchy/__init__.py,sha256=0e0lmGjeb9e7skZy1ksfEOFkwKLIu1N6MnuY1aUWkWA,355
 dclab/rtdc_dataset/fmt_hierarchy/hfilter.py,sha256=niYjYz6R-D2S2zurgmmIqrmsSFJ3tVgAS-UxweImAEU,5852
-dclab/rtdc_dataset/fmt_hierarchy/base.py,sha256=TaDFysJYhRMDDKwVpQn9qcpfmPZofHkvpu46TyHGht4,9440
+dclab/rtdc_dataset/fmt_hierarchy/base.py,sha256=PLmqx-ExfJqVfgVjQNGM6jQ5r9b-zA-t4NwWzrk1ank,9468
 dclab/rtdc_dataset/fmt_hdf5/feat_defect.py,sha256=MeIxPz799x-sljbmSb0n40eVLw_iPnbCfOm07_lTBxo,6540
 dclab/rtdc_dataset/fmt_hdf5/basin.py,sha256=mJZR92Qoa71EwDVDYAP9KtOcjvRyjtA2wO1DkCBfBQc,792
-dclab/rtdc_dataset/fmt_hdf5/events.py,sha256=JUuPviS4lEXMjfNgJE-jkeArAwUVkdA1bmAszJGjPvc,8231
+dclab/rtdc_dataset/fmt_hdf5/events.py,sha256=uJFMSkP8f-cmNdzC4X2LDayw2Q1P1k9qV252TmzC5h8,8179
 dclab/rtdc_dataset/fmt_hdf5/__init__.py,sha256=yWLYK-Fq0EYnp2eYfl1Ze02RBMOWg-iALJWs4dFSxxY,270
 dclab/rtdc_dataset/fmt_hdf5/logs.py,sha256=-mDewfv_aOeHaJykuJIWsqr9a7-moKhoGhqw9cR4ebg,1004
 dclab/rtdc_dataset/fmt_hdf5/tables.py,sha256=G226awNz7NA2V9l1F6jCeyVcJ8V4AJgLYhOfG1Q_5t8,872
-dclab/rtdc_dataset/fmt_hdf5/base.py,sha256=_PgmDq2K7RGCuhV9J4YZwg9noW1hi2w14ZP8ooRR8Lw,6391
+dclab/rtdc_dataset/fmt_hdf5/base.py,sha256=bwbbdt2FXniYANsR1dUF_zeUqT5ByGVv5KfEarnDEhw,6206
 dclab/rtdc_dataset/feat_anc_core/af_fl_max_ctc.py,sha256=gV3FqM0AoOHzWwhU45e3fvBb2MwGVadLL6piVW0YF1s,3687
 dclab/rtdc_dataset/feat_anc_core/af_image_contour.py,sha256=39jvhzz2GmfXDYXu1d3kie7tpBzUkUL_JTxfau-2mt8,3531
 dclab/rtdc_dataset/feat_anc_core/__init__.py,sha256=hEWMqg2rmbxW86Fe-dkTD4b0Zmp-dJe6gPsMjspPGXA,464
@@ -129,9 +130,9 @@ dclab/rtdc_dataset/fmt_tdms/event_image.py,sha256=-jp7Z-N91e4ieumYQ1huMicj7PMJqw
 dclab/rtdc_dataset/fmt_tdms/event_trace.py,sha256=Vkym0QKSw2mq1XZl5n8wDkgHXmaZwQGiMAV5AuRSJkE,5215
 dclab/rtdc_dataset/fmt_tdms/exc.py,sha256=WzrMqnyrzp8gsT8Pf7JKqGGv43ewx7d_qgtirURppRI,813
 dclab/rtdc_dataset/fmt_tdms/event_contour.py,sha256=kjo0wJx9F0gmmOOyR0NoLw6VEtSl3h63WXXkcbfnoS8,9627
-dclab-0.62.7.dist-info/RECORD,,
-dclab-0.62.7.dist-info/LICENSE,sha256=1mLfjOTOaeiMSGPJiF5hHnMQfKX88QVeZpCCXwJGj3k,18131
-dclab-0.62.7.dist-info/WHEEL,sha256=7_oe0rMIEoZOpgBhth1WRv0SCKz8pdiUZgyT0NjKRv8,107
-dclab-0.62.7.dist-info/entry_points.txt,sha256=eOpjgznu-eW-9utUpLU-77O5098YyUEgGF3ksGMdtec,273
-dclab-0.62.7.dist-info/top_level.txt,sha256=irvwZMgs1edY1Zj60ZFk7Almb9Zhk4k6E6aC4YPFnnM,6
-dclab-0.62.7.dist-info/METADATA,sha256=1BqvduCczdHqkI1nKU31GJWR24R1dgXK_PSXJyhwWiM,4754
+dclab-2.18.0.dist-info/RECORD,,
+dclab-2.18.0.dist-info/LICENSE,sha256=1mLfjOTOaeiMSGPJiF5hHnMQfKX88QVeZpCCXwJGj3k,18131
+dclab-2.18.0.dist-info/WHEEL,sha256=ywqtsQ8Z6WlogYsNdfJf_6o9TCfmJc_6Wsg5rUQ0DwU,107
+dclab-2.18.0.dist-info/entry_points.txt,sha256=eOpjgznu-eW-9utUpLU-77O5098YyUEgGF3ksGMdtec,273
+dclab-2.18.0.dist-info/top_level.txt,sha256=irvwZMgs1edY1Zj60ZFk7Almb9Zhk4k6E6aC4YPFnnM,6
+dclab-2.18.0.dist-info/METADATA,sha256=WTNyL58XdjHtE11bxXQWGntyi981Fv5pWGaxXshj1Iw,4824

{dclab-0.62.7.dist-info → dclab-2.18.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.3.0)
+Generator: setuptools (74.1.2)
 Root-Is-Purelib: false
 Tag: cp38-cp38-macosx_11_0_arm64
 

dclab/lme4/lme4_template.R

@@ -1,94 +0,0 @@
-require(stats);
-require(lme4);
-
-model_name <- "<MODEL_NAME>"
-cat("OUTPUT model:", model_name, "#*#\n")
-
-func_model <- "feature ~ group + (1 + group | repetition)"
-func_nullmodel <- "feature ~ (1 + group | repetition)"
-
-# These are the feature, group, and repetition arrays that are set by dclab
-# via templates.
-feature <- c(<FEATURES>)
-group <- c(<GROUPS>)
-repetition <- c(<REPETITIONS>)
-
-data <- data.frame(feature, group, repetition)
-
-if (model_name == "glmer+loglink") {
-    Model <- glmer(func_model, data, family=Gamma(link='log'))
-    NullModel <- glmer(func_nullmodel, data, family=Gamma(link='log'))
-} else if (model_name == "lmer") {
-    Model <- lmer(func_model, data)
-    NullModel <- lmer(func_nullmodel, data)
-} else {
-    stop("Invalid model_name:", model_name)
-}
-
-# Anova analysis (increase verbosity by making models global)
-# Using anova is a very conservative way of determining
-# p values.
-res_anova <- anova(Model, NullModel)
-cat("OUTPUT r anova: ")
-res_anova
-cat("#*#\n")
-
-pvalue <- res_anova$"Pr(>Chisq)"[2]
-cat("OUTPUT anova p-value:", pvalue, "#*#\n")
-
-model_summary <- summary(Model)
-cat("OUTPUT r model summary:")
-model_summary
-cat("#*#\n")
-
-model_coefficients <- coef(Model)
-cat("OUTPUT r model coefficients:")
-model_coefficients
-cat("#*#\n")
-
-fe_reps <- model_coefficients$repetition
-
-effects <- data.frame(coef(model_summary))
-
-fe_icept <- effects$Estimate[1]
-
-fe_treat <- effects$Estimate[2]
-
-if (model_name == "glmer+loglink") {
-    # transform back from log
-    fe_treat <- exp(fe_icept + fe_treat) - exp(fe_icept)
-    fe_icept <- exp(fe_icept)
-    fe_reps[, 2] = exp(fe_reps[, 1] + fe_reps[, 2]) - exp(fe_reps[, 1])
-    fe_reps[, 1] = exp(fe_reps[, 1])
-}
-
-cat("OUTPUT fixed effects intercept:", fe_icept, "#*#\n")
-cat("OUTPUT fixed effects treatment:", fe_treat, "#*#\n")
-cat("OUTPUT fixed effects repetitions:")
-fe_reps
-cat("#*#\n")
-
-# convergence
-
-# convergence warnings in lme4
-is_warning_generated <- function(m) {
-  df <- summary(m)
-  !is.null(df$optinfo$conv$lme4$messages) &&
-           grepl('failed to converge', df$optinfo$conv$lme4$messages)
-}
-lme4_not_converged <- is_warning_generated(Model)
-
-# convergence code by the optimizer
-lme4l <- model_summary$optinfo$conv$lme4
-if (length(lme4l) == 0) {
-    # the optimizer probably does not know
-    conv_code <- 0
-} else if (is.null(lme4l$code)) {
-    # NULL means 0
-    conv_code <- 0
-} else {
-    conv_code <- lme4l$code
-}
-
-cat("OUTPUT model converged:", (conv_code == 0) && !lme4_not_converged, "#*#\n")
-cat("OUTPUT lme4 messages:", lme4l$optinfo$conv$lme4$messages, "#*#\n")