dclab 0.64.0__cp311-cp311-win_amd64.whl → 0.64.1__cp311-cp311-win_amd64.whl

dclab/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.64.0'
-__version_tuple__ = version_tuple = (0, 64, 0)
+__version__ = version = '0.64.1'
+__version_tuple__ = version_tuple = (0, 64, 1)

dclab/kde/base.py

@@ -1,6 +1,7 @@
 import warnings
 
 import numpy as np
+from scipy.interpolate import RegularGridInterpolator as RGI
 
 from .methods import bin_width_doane_div5, get_bad_vals, methods
 from .contours import find_contours_level, get_quantile_levels
@@ -316,6 +317,8 @@ class KernelDensityEstimator:
                     yscale="linear"):
         """Evaluate the kernel density estimate for scatter plots
 
+        The KDE is evaluated with the `kde_type` function for every point.
+
         Parameters
         ----------
         xax: str
@@ -332,7 +335,7 @@ class KernelDensityEstimator:
             Additional keyword arguments to the KDE method
         xscale: str
             If set to "log", take the logarithm of the x-values before
-            computing the KDE. This is useful when data are are
+            computing the KDE. This is useful when data are
             displayed on a log-scale. Defaults to "linear".
         yscale: str
             See `xscale`.
@@ -374,3 +377,83 @@ class KernelDensityEstimator:
             density = np.array([])
 
         return density
+
+    def get_at(self, xax="area_um", yax="deform", positions=None,
+               kde_type="histogram", kde_kwargs=None, xscale="linear",
+               yscale="linear"):
+        """Evaluate the kernel density estimate for specific events
+
+        The KDE is computed via linear interpolation from the output
+        of `get_raster`.
+
+        Parameters
+        ----------
+        xax: str
+            Identifier for X axis (e.g. "area_um", "aspect", "deform")
+        yax: str
+            Identifier for Y axis
+        positions: list of two 1d ndarrays or ndarray of shape (2, N)
+            The positions where the KDE will be computed. Note that
+            the KDE estimate is computed from the points that
+            are set in `self.rtdc_ds.filter.all`.
+        kde_type: str
+            The KDE method to use, see :const:`.kde_methods.methods`
+        kde_kwargs: dict
+            Additional keyword arguments to the KDE method
+        xscale: str
+            If set to "log", take the logarithm of the x-values before
+            computing the KDE. This is useful when data are
+            displayed on a log-scale. Defaults to "linear".
+        yscale: str
+            See `xscale`.
+
+        Returns
+        -------
+        density : 1d ndarray
+            The kernel density evaluated for the filtered events.
+        """
+        if kde_kwargs is None:
+            kde_kwargs = {}
+        xax = xax.lower()
+        yax = yax.lower()
+        kde_type = kde_type.lower()
+        if kde_type not in methods:
+            raise ValueError(f"Not a valid kde type: {kde_type}!")
+
+        # Get data
+        x = self.rtdc_ds[xax][self.rtdc_ds.filter.all]
+        y = self.rtdc_ds[yax][self.rtdc_ds.filter.all]
+
+        # Apply scale (no change for linear scale)
+        xs = self.apply_scale(x, xscale, xax)
+        ys = self.apply_scale(y, yscale, yax)
+
+        if positions:
+            xs = self.apply_scale(positions[0], xscale, xax)
+            ys = self.apply_scale(positions[1], yscale, yax)
+
+        if len(x):
+            xr, yr, density_grid = self.get_raster(xax=xax,
+                                                   yax=yax,
+                                                   kde_type=kde_type,
+                                                   kde_kwargs=kde_kwargs,
+                                                   xscale=xscale,
+                                                   yscale=yscale)
+
+            # Apply scale (no change for linear scale)
+            xrs = self.apply_scale(xr, xscale, xax)
+            yrs = self.apply_scale(yr, yscale, yax)
+
+            # 'scipy.interp2d' has been removed in SciPy 1.14.0
+            # https://scipy.github.io/devdocs/tutorial/interpolate/interp_transition_guide.html
+            interp_func = RGI((xrs[:, 0], yrs[0, :]),
+                              density_grid,
+                              method="linear",
+                              bounds_error=False,
+                              fill_value=np.nan)
+            density = interp_func((xs, ys))
+
+        else:
+            density = np.array([])
+
+        return density

dclab/statistics.py

@@ -86,7 +86,7 @@ def flow_rate(ds):
         return np.nan
 
 
-def get_statistics(ds, methods=None, features=None):
+def get_statistics(ds, methods=None, features=None, ret_dict=False):
     """Compute statistics for an RT-DC dataset
 
     Parameters
@@ -96,13 +96,16 @@ def get_statistics(ds, methods=None, features=None):
     methods: list of str or None
         The methods wih which to compute the statistics.
         The list of available methods is given with
-        `dclab.statistics.Statistics.available_methods.keys()`
+        :func:`.available_methods.keys`
         If set to `None`, statistics for all methods are computed.
     features: list of str
         Feature name identifiers are defined by
-        `dclab.definitions.feature_exists`.
+        :func:`dclab.definitions.feature_exists`.
         If set to `None`, statistics for all scalar features
         available are computed.
+    ret_dict: bool
+        Instead of returning ``(header, values)``, return a dictionary
+        with headers as keys.
 
     Returns
     -------
@@ -148,7 +151,10 @@ def get_statistics(ds, methods=None, features=None):
                 label = dfn.get_feature_label(ft, rtdc_ds=ds)
                 header.append(" ".join([mt, label]))
 
-    return header, values
+    if ret_dict:
+        return dict(zip(header, values))
+    else:
+        return header, values
 
 
 def mode(data):
@@ -191,7 +197,24 @@ def mode(data):
 # Register all the methods
 # Methods that require an axis
 Statistics(name="Mean",   req_feature=True, method=np.average)
+# Premature-Optimization warning: `np.percentile` also accepts an array
+# of percentiles as the `q` argument, which I would expect to yield better
+# performance than computing percentiles individually. Implementing this
+# would break the way we are defining statistical methods here (One
+# `Statistics` instance per method) and thus requires a considerable
+# amount of work (much more work than writing this text here). It would
+# also make understanding the code more difficult. In addition, computing
+# statistics is not done often and is extremely fast anyway for a few
+# millions of events. Don't optimize this!
+Statistics(name="10th Percentile", req_feature=True,
+           method=lambda data: np.percentile(data, 10))
+Statistics(name="25th Percentile", req_feature=True,
+           method=lambda data: np.percentile(data, 25))
 Statistics(name="Median", req_feature=True, method=np.median)
+Statistics(name="75th Percentile", req_feature=True,
+           method=lambda data: np.percentile(data, 75))
+Statistics(name="90th Percentile", req_feature=True,
+           method=lambda data: np.percentile(data, 90))
 Statistics(name="Mode",   req_feature=True, method=mode)
 Statistics(name="SD",     req_feature=True, method=np.std)
 # Methods that work on RTDCBase

{dclab-0.64.0.dist-info → dclab-0.64.1.dist-info}/METADATA

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: dclab
-Version: 0.64.0
+Version: 0.64.1
 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>
-License: GPL-2.0-or-later
+License-Expression: GPL-2.0-or-later
 Project-URL: source, https://github.com/DC-Analysis/dclab
 Project-URL: tracker, https://github.com/DC-Analysis/dclab/issues
 Project-URL: documentation, https://dclab.readthedocs.io/en/stable/

{dclab-0.64.0.dist-info → dclab-0.64.1.dist-info}/RECORD

@@ -1,13 +1,13 @@
 dclab/__init__.py,sha256=kSr6VI0UI-beS9beOEpERTUAV1NINHx_G6u1VmBm9D8,1624
-dclab/_version.py,sha256=0j6jwYqVbZkAlg02f-8H_THxmeCYIPDxuOyC8QfwGHg,534
+dclab/_version.py,sha256=mXVRd4XXSvubXnCvvibtN_3CiyIT4FFBF_TNPrxM6fk,534
 dclab/cached.py,sha256=t01BYTf43VEsBYa0c-bMxgceF5vKoGV73b42UlLH6Lo,3014
-dclab/downsampling.cp311-win_amd64.pyd,sha256=Tq1VQF3-aAuQbSio1tpjr8JjCZ8EvNscl-YMJYnrVM4,169984
+dclab/downsampling.cp311-win_amd64.pyd,sha256=1zkkvDZVFA-MarNlbVazghDgze7d5S9uXTL2mp3GDKA,170496
 dclab/downsampling.pyx,sha256=Ez6MbNbzCUzs2IXXKtAYsjtYqP22kI8hdA1IE-3mqvY,7488
 dclab/http_utils.py,sha256=aIW4ATmyk02AjQmoTm7mAWdsaQD1siEPLx47IlEcYls,11234
 dclab/kde_contours.py,sha256=cYeBtvbBqLHCz5W8AiEAAd9O3yLsSBbLcRVj1WZ1pRo,288
 dclab/kde_methods.py,sha256=tY82WQsX2_5_Szb7zma9yQD-HxCg2fAkMvNs-K05jMQ,376
 dclab/polygon_filter.py,sha256=C4uBvK8zzT8irUOIgITvASlCtc0EEMM5edp4dFx-9jw,13878
-dclab/statistics.py,sha256=6saNuiXCcYmI8_cmb8Tb7E34BbsxHzTvNNlbKeNoDIw,6558
+dclab/statistics.py,sha256=nluuzl9h-RokxpsYLFLTAx6gnt6ArBhmQJffZbeIlac,7824
 dclab/util.py,sha256=X9LqxrEJNClzPSko49MMsz2MlybLwkButqqQmxfnj44,6036
 dclab/warn.py,sha256=pv_W9cKBJg-mUn-_6O4xBwRmwI9QaEIW9EBEIiyL0iU,538
 dclab/cli/__init__.py,sha256=IB33_cscv866CAwXnP1ZO9tlBpOldB0UQuR5P87FmSQ,493
@@ -35,14 +35,14 @@ dclab/external/packaging/version.py,sha256=NgEgv7me4UCvFMyiNYD-nc_28b9UHUvBVh8RD
 dclab/external/skimage/LICENSE,sha256=Tdv08zzxYV32WRdYnco9P3nVyS5w17OTxIAFeRSd1wc,1480
 dclab/external/skimage/__init__.py,sha256=icOIlThkyn_hxmnM_i7OpbU7fhvqYWNpGdNGD38qthU,74
 dclab/external/skimage/_find_contours.py,sha256=auRMNfZg7B73DX7kPXxgD8gMXXB3Lk9QDWt4wlQnUWg,9556
-dclab/external/skimage/_find_contours_cy.cp311-win_amd64.pyd,sha256=yWP17yqiQHy8_mhH9vFxZltRF_8uM5x-Lo0UeFyAKEk,130560
+dclab/external/skimage/_find_contours_cy.cp311-win_amd64.pyd,sha256=RNLFzsG6KBMS3XehjxaFj-s4OFa6D4gRCUa7P__oNX8,131072
 dclab/external/skimage/_find_contours_cy.pyx,sha256=c-EobLhKjZNCpuqWxmvrcH35uAY_Bu-_hZiUHbXODms,7349
-dclab/external/skimage/_pnpoly.cp311-win_amd64.pyd,sha256=JNYo9E6tHmdJUgHXqKY49uXr96AeZ3Ds_RmgjHsh0cs,144384
+dclab/external/skimage/_pnpoly.cp311-win_amd64.pyd,sha256=ttMj3Jk-h6NDRCD3ngRGPjDOU51Q-EFuU5XD1wR3o6I,144896
 dclab/external/skimage/_pnpoly.pyx,sha256=eHV3DlIGcBhAQ12-Y58EYq8xcq0Sibyc4xTxzX9NJsk,2603
 dclab/external/skimage/measure.py,sha256=rzyI0HCr9O9GJNieVW8pcqDjTGRAdSehDUawD8QkIAE,254
 dclab/external/skimage/pnpoly.py,sha256=zB4rSxjHJyY1OsGZ7QfFQqxIEDLGK8CWPehwutoFqm4,1400
 dclab/external/skimage/_shared/__init__.py,sha256=q29esTsNh0HfQxcd2EuwdYNbEBJwo_qY4dfv7RihzoA,38
-dclab/external/skimage/_shared/geometry.cp311-win_amd64.pyd,sha256=BrdRvUc9AJWt39wkohryFuclAI7MIdBhZNWIQUOfz6o,19456
+dclab/external/skimage/_shared/geometry.cp311-win_amd64.pyd,sha256=_qenxbnbWLM2ll3e5ZW0HLJnRvn3WLx_xEFAB5-CU0U,19456
 dclab/external/skimage/_shared/geometry.pxd,sha256=3gJ7fbXXsxJunSN4biE0dzEbZpX9ZqzR4cUDDN0JnAU,352
 dclab/external/skimage/_shared/geometry.pyx,sha256=b6hADE8chse63haO1Kdt13_oQ54J9tkBf7dVA22-s-M,1722
 dclab/external/statsmodels/LICENSE,sha256=8D7nwukc6YgsZCdN9mG0psM3I9j-z8fuUgFyVhnMXpU,1672
@@ -76,7 +76,7 @@ dclab/isoelastics/iso_LE-2D-FEM-19-area_um-deform.txt,sha256=lcTjUUnIwj_bVBrG2T2
 dclab/isoelastics/iso_LE-2D-FEM-19-volume-deform.txt,sha256=vTcazOlOXo3BQ0NQtGB_IdHKA0neOLXZ_d3JuMU--RE,83358
 dclab/isoelastics/iso_LE-2D-ana-18-area_um-deform.txt,sha256=KD2RkhCfkrna20pLJ3UzNZZapMkhQydMYz0iKdMtRRE,46805
 dclab/kde/__init__.py,sha256=A7GXfOI-6HNxD1ljkmnU9NjkFhoT2_WxlPmJa29PLm0,56
-dclab/kde/base.py,sha256=ZfCIWzWg4LH-B7k0q1uWleH0zbBJv0olnF2evynQZ2c,13337
+dclab/kde/base.py,sha256=mp3xnPCqA5hP1aD3Owa9U3SxfrnTGTk_hKPuuBlFtw8,16655
 dclab/kde/contours.py,sha256=vWx34Zxe9CuKd255Lje67pYEYZsLrCVPNopf_dHanL8,6964
 dclab/kde/methods.py,sha256=diRNGM7U91UHEGMaee2PcxSegQ9OGUPVt6McI7DhCFM,9751
 dclab/lme4/__init__.py,sha256=85rlF3G9ZblRue7SB2DrMqSfVPVyE37ujr55Oy7OZaI,277
@@ -134,9 +134,9 @@ dclab/rtdc_dataset/fmt_tdms/event_mask.py,sha256=cW-Tw2PIe6X1Hc4UZJ22-mI_qFaIMWA
 dclab/rtdc_dataset/fmt_tdms/event_trace.py,sha256=ktWnXfMir1v5Wfeo7tOd0txSOe1bgsXotf9Ul5T5-B4,5361
 dclab/rtdc_dataset/fmt_tdms/exc.py,sha256=FfxUY4LGIMPGJTYmGITmEm7X5iu8GBsj7OfZR8Zb-IE,850
 dclab/rtdc_dataset/fmt_tdms/naming.py,sha256=SFeWiwIN7sg0qNe0Aya2bZshN1Zbw4YcOKunZ6kfIGM,5524
-dclab-0.64.0.dist-info/licenses/LICENSE,sha256=Aq3cYb2xLk3Y_aIOhaoZxi8FlVeMVs3-3FMEBvAEixM,15643
-dclab-0.64.0.dist-info/METADATA,sha256=5nq9U2WWCWAlhgIEJLU4bA512Ycrly7A2Hmqa9y6fSM,4902
-dclab-0.64.0.dist-info/WHEEL,sha256=qxRMWkcfC6EPKglFaripnDVKofxBh0a8FNl-gKWx4zc,101
-dclab-0.64.0.dist-info/entry_points.txt,sha256=eOpjgznu-eW-9utUpLU-77O5098YyUEgGF3ksGMdtec,273
-dclab-0.64.0.dist-info/top_level.txt,sha256=irvwZMgs1edY1Zj60ZFk7Almb9Zhk4k6E6aC4YPFnnM,6
-dclab-0.64.0.dist-info/RECORD,,
+dclab-0.64.1.dist-info/licenses/LICENSE,sha256=Aq3cYb2xLk3Y_aIOhaoZxi8FlVeMVs3-3FMEBvAEixM,15643
+dclab-0.64.1.dist-info/METADATA,sha256=g2ygLFICqk7MKmTDzdSZIdHfR4YVuCpqytG8HSy69qo,4913
+dclab-0.64.1.dist-info/WHEEL,sha256=JLOMsP7F5qtkAkINx5UnzbFguf8CqZeraV8o04b0I8I,101
+dclab-0.64.1.dist-info/entry_points.txt,sha256=eOpjgznu-eW-9utUpLU-77O5098YyUEgGF3ksGMdtec,273
+dclab-0.64.1.dist-info/top_level.txt,sha256=irvwZMgs1edY1Zj60ZFk7Almb9Zhk4k6E6aC4YPFnnM,6
+dclab-0.64.1.dist-info/RECORD,,

{dclab-0.64.0.dist-info → dclab-0.64.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.7.1)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: false
 Tag: cp311-cp311-win_amd64