dclab 0.64.0__cp311-cp311-macosx_10_9_x86_64.whl → 0.64.1__cp311-cp311-macosx_10_9_x86_64.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

@@ -1,6 +1,6 @@
 dclab/kde_methods.py,sha256=f0-zDN7ETintvGB3gSzxwgBb53YtT9jZtzI70EAX50g,365
-dclab/downsampling.cpython-311-darwin.so,sha256=SPJAWHzksA12gLjp9SiomYxybLPvjXeIukCZPvJjRso,236984
-dclab/_version.py,sha256=zVb-mNfv7Q80VP6gLIonMXNXR1BAme5zhf4Ww25kC90,513
+dclab/downsampling.cpython-311-darwin.so,sha256=uKkV17PIwJz0sJRNAIPJVoko5vfiwOffs8peakr4k60,237616
+dclab/_version.py,sha256=9r4reeZylDKkIG06-4LPXZLfHirJkjSSEYOAOeaEme8,513
 dclab/util.py,sha256=HFT5ZQV6AW8GIIruVMldukbVVdlMyKH50GUfOogAcxI,5860
 dclab/downsampling.pyx,sha256=OK7zbgGLl5gVyoU8ZBHo9EWwb8C9ChavmLNEvQvC9T0,7258
 dclab/__init__.py,sha256=wyJWhElQRPcq09vUqUnuquTU_KHgHxv6wQxuxQ988Iw,1583
@@ -8,7 +8,7 @@ dclab/warn.py,sha256=MjJvyQeuvIXFQ2-fHDzbmXJ0scnHqqRJlIxfuLI_utE,523
 dclab/cached.py,sha256=eWTYBiI-HQM7JuPH-oxa5LLnhAX32GpRwlYg2kQ3sTA,2917
 dclab/http_utils.py,sha256=XHicbHQts5LY3zSNmYqNgAZpKTktotEiwQgJ8d2sBlk,10912
 dclab/polygon_filter.py,sha256=qexmo-rXe06CUPZhN6EMJy4y4B5gXZeqejdvIB2arOE,13480
-dclab/statistics.py,sha256=tJDqPlY_Jw2Hhl-s7ugMBSZAxcRuPu4LQuBAZBXz7t8,6355
+dclab/statistics.py,sha256=DWBG_Kj7cn89b_s5mqWYDCMGB881jHcCRFY-KAOBnhE,7598
 dclab/kde_contours.py,sha256=UlU64lrzMQUZH11oZndW7xf7NFCzwP3FcVujwuqXDCI,278
 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
@@ -50,7 +50,7 @@ dclab/cli/task_compress.py,sha256=LH3j41aKq5regAH-ZFdOgnXImf5DrReDJ7ITwUObUSQ,41
 dclab/kde/contours.py,sha256=WoRqBj_xK-23FZjtaYly7E2Q8sGZ16q2ILq-DmrlmC8,6742
 dclab/kde/methods.py,sha256=8g4lYUKYqt2pdA9efHVRBDCUUzmePmWPp6rljtJ0XD8,9438
 dclab/kde/__init__.py,sha256=_WSLPMfxE2su6tmO5mJxUE_9ON16-pqQUQCUlzRtyKI,55
-dclab/kde/base.py,sha256=KuV_9_AJ4Sn14C4WAH4eF63URAVYCnaFOcLgsVCaAjo,12961
+dclab/kde/base.py,sha256=w0or7ix8hnK-xqtGSyhyn48YUo55WnEEPsBjWrJna9s,16196
 dclab/external/__init__.py,sha256=gb0UdzoMymEURPsTXRqVTT1ZJedJ2ubH3jApBIRkwjk,93
 dclab/external/packaging/version.py,sha256=9MLL6_EYHvGA1yCGndwL5ZmmDA_wqQsW15GyKrI6siQ,14685
 dclab/external/packaging/LICENSE,sha256=ytHvW9NA1z4HS6YU0m996spceUDD2MNIUuZcSQlobEg,197
@@ -70,11 +70,11 @@ dclab/external/skimage/pnpoly.py,sha256=r8hFNiTz5XlUoNZjosqA0iyv1FPn0l7ewbplgFgk
 dclab/external/skimage/_find_contours.py,sha256=16v5eeTZBmevG8SSuXtJ6yUpVPhwfSmtc8pDD0nuuOU,9340
 dclab/external/skimage/__init__.py,sha256=-B2QUKHAFzQuBWuuKvPDC5JIl0Zb-x3OGmbwPaE9VwQ,72
 dclab/external/skimage/_pnpoly.pyx,sha256=Qdn6xPazDschBqbr46DzB75MB2MnqvdnoTSBMK7kUGE,2504
-dclab/external/skimage/_find_contours_cy.cpython-311-darwin.so,sha256=KXnlFOHj_uQ__xskIdI1YnEsvUXi_NsmtMIlcVul9kc,188720
+dclab/external/skimage/_find_contours_cy.cpython-311-darwin.so,sha256=FpittJbhwCXhLudTVAzi45uM1yMeharQzYgBoT4E8l4,189352
 dclab/external/skimage/_find_contours_cy.pyx,sha256=pZJOBhMHzYEMkcz4WQVyjn7jDNrdjCfet47FU1hRAxk,7161
-dclab/external/skimage/_pnpoly.cpython-311-darwin.so,sha256=mwAi1m2UnUKjJxPcBu2OdKz7jNU3jegRtLjzzlNGEho,194192
+dclab/external/skimage/_pnpoly.cpython-311-darwin.so,sha256=-XGCpbXeNzPxQrHmoIT_-aSV3I1tE_oH47zgDMrbspU,194824
 dclab/external/skimage/_shared/geometry.pxd,sha256=kRsu9ifv_rL3kbRIgSLf86p0hn2oTMp6s013lZ9bBZM,346
-dclab/external/skimage/_shared/geometry.cpython-311-darwin.so,sha256=mN7l27MiiDAEssQ4PDOCGYwFZnsxE12AgfomAjVWgZg,38320
+dclab/external/skimage/_shared/geometry.cpython-311-darwin.so,sha256=W3HYe3Ri6ZRPsQqOyilrLlem965_nbRvnpH0DjQ1Ycw,38320
 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
@@ -134,9 +134,9 @@ 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-0.64.0.dist-info/RECORD,,
-dclab-0.64.0.dist-info/WHEEL,sha256=osp_SOLYJPdNJIHZoUXoIdnwmLNnAVt6RayTuFLQ60s,137
-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/METADATA,sha256=zfrjZaLGPiE_ZPYkVtoUGvGI-CPkjgY-eiKJshd-3bo,4755
-dclab-0.64.0.dist-info/licenses/LICENSE,sha256=gLDaVZWRrlnLdyfOrR0qfWjLbOVcjvoJ-kCLUK0fyXA,15360
+dclab-0.64.1.dist-info/RECORD,,
+dclab-0.64.1.dist-info/WHEEL,sha256=TY6wS7uh4kKn2hb4-XnLjkub5JFV8id422w1jhyVjcQ,137
+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/METADATA,sha256=WoNkTGPhcp_6fJpJQ2r9HPAJoxE_lRtwE4mQGj56tCE,4766
+dclab-0.64.1.dist-info/licenses/LICENSE,sha256=gLDaVZWRrlnLdyfOrR0qfWjLbOVcjvoJ-kCLUK0fyXA,15360

{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-macosx_10_9_x86_64
 Generator: delocate 0.13.0