dclab 0.64.0__cp311-cp311-macosx_11_0_arm64.whl → 0.64.2__cp311-cp311-macosx_11_0_arm64.whl
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- dclab/_version.py +2 -2
- dclab/definitions/feat_logic.py +27 -28
- dclab/downsampling.cpython-311-darwin.so +0 -0
- dclab/external/skimage/_find_contours_cy.cpython-311-darwin.so +0 -0
- dclab/external/skimage/_pnpoly.cpython-311-darwin.so +0 -0
- dclab/external/skimage/_shared/geometry.cpython-311-darwin.so +0 -0
- dclab/kde/base.py +84 -1
- dclab/rtdc_dataset/core.py +3 -3
- dclab/rtdc_dataset/feat_basin.py +27 -15
- dclab/statistics.py +27 -4
- {dclab-0.64.0.dist-info → dclab-0.64.2.dist-info}/METADATA +2 -2
- {dclab-0.64.0.dist-info → dclab-0.64.2.dist-info}/RECORD +16 -16
- {dclab-0.64.0.dist-info → dclab-0.64.2.dist-info}/WHEEL +1 -1
- {dclab-0.64.0.dist-info → dclab-0.64.2.dist-info}/entry_points.txt +0 -0
- {dclab-0.64.0.dist-info → dclab-0.64.2.dist-info}/licenses/LICENSE +0 -0
- {dclab-0.64.0.dist-info → dclab-0.64.2.dist-info}/top_level.txt +0 -0
dclab/_version.py
CHANGED
dclab/definitions/feat_logic.py
CHANGED
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@@ -1,6 +1,11 @@
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import re
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from . import feat_const
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ML_SCORE_REGEX = re.compile(r"^ml_score_[a-z0-9]{3}$")
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def check_feature_shape(name, data):
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"""Check if (non)-scalar feature matches with its data's dimensionality
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@@ -17,11 +22,15 @@ def check_feature_shape(name, data):
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If the data's shape does not match its scalar description
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"""
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if len(data.shape) == 1 and not scalar_feature_exists(name):
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raise ValueError(
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raise ValueError(
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f"Feature '{name}' is not a scalar feature, but "
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"a 1D array was given for `data`!"
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)
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elif len(data.shape) != 1 and scalar_feature_exists(name):
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raise ValueError(
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raise ValueError(
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f"Feature '{name}' is a scalar feature, but the "
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"`data` array is not 1D!"
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)
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def feature_exists(name, scalar_only=False):
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@@ -56,15 +65,9 @@ def feature_exists(name, scalar_only=False):
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elif not scalar_only and name in feat_const.feature_names:
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# non-scalar feature
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valid = True
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#
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if (name.startswith("ml_score_")
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and len(name) == len("ml_score_???")
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and name[-3] in valid_chars
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and name[-2] in valid_chars
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and name[-1] in valid_chars):
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valid = True
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elif ML_SCORE_REGEX.match(name):
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# machine-learning score feature ml_score_???
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valid = True
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return valid
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@@ -93,8 +96,10 @@ def feature_register(name, label=None, is_scalar=True):
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allowed_chars = "abcdefghijklmnopqrstuvwxyz_1234567890"
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feat = "".join([f for f in name if f in allowed_chars])
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if feat != name:
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raise ValueError(
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raise ValueError(
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"`feature` must only contain lower-case characters, "
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f"digits, and underscores; got '{name}'!"
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)
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if label is None:
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label = f"User-defined feature {name}"
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if feature_exists(name):
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@@ -156,22 +161,16 @@ def get_feature_label(name, rtdc_ds=None, with_unit=True):
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TODO: extract feature label from ancillary information when an rtdc_ds is
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given.
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"""
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# TODO: Is there another way of avoiding this circular import?
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from ..rtdc_dataset.feat_anc_core.ancillary_feature import AncillaryFeature
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assert feature_exists(name)
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if name in feat_const.feature_name2label:
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label = feat_const.feature_name2label[name]
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elif ML_SCORE_REGEX.match(name):
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# use a generic name for machine-learning features
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label = f"ML score {name[-3:].upper()}"
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else:
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labelid = af.data.outputs.index(name)
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label = af.data.output_labels[labelid]
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break
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else:
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# If that did not work, use a generic name.
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label = "ML score {}".format(name[-3:].upper())
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exists = feature_exists(name)
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msg = f"Could not find label for '{name}'"
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msg += " (feature does not exist)" if not exists else ""
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raise ValueError(msg)
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if not with_unit:
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if label.endswith("]") and label.count("["):
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label = label.rsplit("[", 1)[0].strip()
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dclab/kde/base.py
CHANGED
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import warnings
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import numpy as np
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from scipy.interpolate import RegularGridInterpolator as RGI
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from .methods import bin_width_doane_div5, get_bad_vals, methods
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from .contours import find_contours_level, get_quantile_levels
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yscale="linear"):
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"""Evaluate the kernel density estimate for scatter plots
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The KDE is evaluated with the `kde_type` function for every point.
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Parameters
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----------
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xax: str
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Additional keyword arguments to the KDE method
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xscale: str
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If set to "log", take the logarithm of the x-values before
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computing the KDE. This is useful when data are
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computing the KDE. This is useful when data are
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displayed on a log-scale. Defaults to "linear".
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yscale: str
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See `xscale`.
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density = np.array([])
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return density
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def get_at(self, xax="area_um", yax="deform", positions=None,
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kde_type="histogram", kde_kwargs=None, xscale="linear",
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yscale="linear"):
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"""Evaluate the kernel density estimate for specific events
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The KDE is computed via linear interpolation from the output
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of `get_raster`.
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Parameters
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----------
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xax: str
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Identifier for X axis (e.g. "area_um", "aspect", "deform")
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yax: str
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Identifier for Y axis
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positions: list of two 1d ndarrays or ndarray of shape (2, N)
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The positions where the KDE will be computed. Note that
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the KDE estimate is computed from the points that
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are set in `self.rtdc_ds.filter.all`.
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kde_type: str
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The KDE method to use, see :const:`.kde_methods.methods`
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kde_kwargs: dict
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Additional keyword arguments to the KDE method
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xscale: str
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If set to "log", take the logarithm of the x-values before
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computing the KDE. This is useful when data are
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displayed on a log-scale. Defaults to "linear".
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yscale: str
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See `xscale`.
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Returns
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-------
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density : 1d ndarray
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The kernel density evaluated for the filtered events.
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"""
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kde_kwargs = {}
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xax = xax.lower()
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yax = yax.lower()
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kde_type = kde_type.lower()
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if kde_type not in methods:
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raise ValueError(f"Not a valid kde type: {kde_type}!")
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# Get data
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# Apply scale (no change for linear scale)
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if positions:
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kde_kwargs=kde_kwargs,
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xscale=xscale,
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yscale=yscale)
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# Apply scale (no change for linear scale)
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yrs = self.apply_scale(yr, yscale, yax)
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# 'scipy.interp2d' has been removed in SciPy 1.14.0
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# https://scipy.github.io/devdocs/tutorial/interpolate/interp_transition_guide.html
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interp_func = RGI((xrs[:, 0], yrs[0, :]),
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density_grid,
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method="linear",
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bounds_error=False,
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fill_value=np.nan)
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density = interp_func((xs, ys))
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else:
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density = np.array([])
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return density
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dclab/rtdc_dataset/core.py
CHANGED
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identifier = self.config.get("experiment", {}).get("run identifier",
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None)
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date = self.config.get("experiment", {}).get("date", None)
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sid = self.config.get("setup", {}).get("identifier", None)
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time = self.config.get("experiment", {}).get("time", None) or None
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date = self.config.get("experiment", {}).get("date", None) or None
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# only compute an identifier if all of the above are defined.
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dclab/rtdc_dataset/feat_basin.py
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# No measurement identifier was presented by the
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# referencing dataset.
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# referencing dataset. We are in the dark.
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# Don't perform any checks.
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basin_identifier = self.get_measurement_identifier()
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if basin_identifier is None:
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# Again, we are in the dark, because the basin dataset
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# does not have an identifier. This is an undesirable
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# situation, but there is nothing we can do about it.
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if self.mapping == "same":
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# When we have identical mapping, then the
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# measurement identifier has to match exactly.
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verifier = str.__eq__
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else:
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# When we have non-identical mapping (e.g. exported
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# data), then the measurement identifier has to
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# partially match.
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verifier = str.startswith
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self._measurement_identifier_verified = verifier(
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self.measurement_identifier, basin_identifier)
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check_rid = self._measurement_identifier_verified
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check_rid = True
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@@ -538,8 +546,12 @@ class BasinProxy:
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def __getitem__(self, feat):
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if feat not in self._features:
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if feat == "contour":
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raise NotImplementedError("Feature 'contour' cannot be "
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"handled by BasinProxy.")
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else:
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feat_obj = BasinProxyFeature(feat_obj=self.ds[feat],
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basinmap=self.basinmap)
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self._features[feat] = feat_obj
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return self._features[feat]
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dclab/statistics.py
CHANGED
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def get_statistics(ds, methods=None, features=None):
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def get_statistics(ds, methods=None, features=None, ret_dict=False):
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"""Compute statistics for an RT-DC dataset
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Parameters
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@@ -96,13 +96,16 @@ def get_statistics(ds, methods=None, features=None):
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methods: list of str or None
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The methods wih which to compute the statistics.
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The list of available methods is given with
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:func:`.available_methods.keys`
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If set to `None`, statistics for all methods are computed.
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features: list of str
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Feature name identifiers are defined by
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:func:`dclab.definitions.feature_exists`.
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If set to `None`, statistics for all scalar features
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available are computed.
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ret_dict: bool
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Instead of returning ``(header, values)``, return a dictionary
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with headers as keys.
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-------
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label = dfn.get_feature_label(ft, rtdc_ds=ds)
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header.append(" ".join([mt, label]))
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return header, values
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# Register all the methods
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Statistics(name="Mean", req_feature=True, method=np.average)
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# Premature-Optimization warning: `np.percentile` also accepts an array
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# of percentiles as the `q` argument, which I would expect to yield better
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# performance than computing percentiles individually. Implementing this
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# would break the way we are defining statistical methods here (One
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# `Statistics` instance per method) and thus requires a considerable
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# amount of work (much more work than writing this text here). It would
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# also make understanding the code more difficult. In addition, computing
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# statistics is not done often and is extremely fast anyway for a few
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# millions of events. Don't optimize this!
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Statistics(name="10th Percentile", req_feature=True,
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method=lambda data: np.percentile(data, 10))
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Statistics(name="25th Percentile", req_feature=True,
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method=lambda data: np.percentile(data, 25))
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Statistics(name="75th Percentile", req_feature=True,
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method=lambda data: np.percentile(data, 75))
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Statistics(name="90th Percentile", req_feature=True,
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method=lambda data: np.percentile(data, 90))
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Statistics(name="Mode", req_feature=True, method=mode)
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# Methods that work on RTDCBase
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1
1
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Metadata-Version: 2.4
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2
2
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Name: dclab
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-
Version: 0.64.
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Version: 0.64.2
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Summary: Library for real-time deformability cytometry (RT-DC)
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Author: Benedikt Hartmann, Eoghan O'Connell, Maik Herbig, Maximilian Schlögel, Nadia Sbaa, Paul Müller, Philipp Rosendahl, Raghava Alajangi
|
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Maintainer-email: Paul Müller <dev@craban.de>
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License: GPL-2.0-or-later
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7
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License-Expression: GPL-2.0-or-later
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Project-URL: source, https://github.com/DC-Analysis/dclab
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Project-URL: tracker, https://github.com/DC-Analysis/dclab/issues
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dclab/kde_methods.py,sha256=f0-zDN7ETintvGB3gSzxwgBb53YtT9jZtzI70EAX50g,365
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dclab/downsampling.cpython-311-darwin.so,sha256=
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dclab/_version.py,sha256=
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dclab/downsampling.cpython-311-darwin.so,sha256=RI-gzLhVjwbOw0ZBt0JhZPjrxE_WGlTgXeOUIuc_YEI,244000
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+
dclab/_version.py,sha256=mnIFaYC6sZ_j_i-gY87R5meP1KGPhfa0o-8iIIlF24U,513
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dclab/util.py,sha256=HFT5ZQV6AW8GIIruVMldukbVVdlMyKH50GUfOogAcxI,5860
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dclab/downsampling.pyx,sha256=OK7zbgGLl5gVyoU8ZBHo9EWwb8C9ChavmLNEvQvC9T0,7258
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dclab/__init__.py,sha256=wyJWhElQRPcq09vUqUnuquTU_KHgHxv6wQxuxQ988Iw,1583
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dclab/cached.py,sha256=eWTYBiI-HQM7JuPH-oxa5LLnhAX32GpRwlYg2kQ3sTA,2917
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dclab/http_utils.py,sha256=XHicbHQts5LY3zSNmYqNgAZpKTktotEiwQgJ8d2sBlk,10912
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dclab/polygon_filter.py,sha256=qexmo-rXe06CUPZhN6EMJy4y4B5gXZeqejdvIB2arOE,13480
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dclab/statistics.py,sha256=
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dclab/statistics.py,sha256=DWBG_Kj7cn89b_s5mqWYDCMGB881jHcCRFY-KAOBnhE,7598
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dclab/kde_contours.py,sha256=UlU64lrzMQUZH11oZndW7xf7NFCzwP3FcVujwuqXDCI,278
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dclab/isoelastics/iso_LE-2D-FEM-19-volume-deform.txt,sha256=vTcazOlOXo3BQ0NQtGB_IdHKA0neOLXZ_d3JuMU--RE,83358
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|
dclab/isoelastics/iso_HE-3D-FEM-22-area_um-deform.txt,sha256=IjULG1KO-hClaYPoJJnwPbF2TkS9i9jxF1tbhhQTClY,71350
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@@ -50,7 +50,7 @@ dclab/cli/task_compress.py,sha256=LH3j41aKq5regAH-ZFdOgnXImf5DrReDJ7ITwUObUSQ,41
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dclab/kde/contours.py,sha256=WoRqBj_xK-23FZjtaYly7E2Q8sGZ16q2ILq-DmrlmC8,6742
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dclab/kde/methods.py,sha256=8g4lYUKYqt2pdA9efHVRBDCUUzmePmWPp6rljtJ0XD8,9438
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dclab/kde/__init__.py,sha256=_WSLPMfxE2su6tmO5mJxUE_9ON16-pqQUQCUlzRtyKI,55
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dclab/kde/base.py,sha256=
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dclab/kde/base.py,sha256=w0or7ix8hnK-xqtGSyhyn48YUo55WnEEPsBjWrJna9s,16196
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dclab/external/__init__.py,sha256=gb0UdzoMymEURPsTXRqVTT1ZJedJ2ubH3jApBIRkwjk,93
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dclab/external/packaging/version.py,sha256=9MLL6_EYHvGA1yCGndwL5ZmmDA_wqQsW15GyKrI6siQ,14685
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dclab/external/packaging/LICENSE,sha256=ytHvW9NA1z4HS6YU0m996spceUDD2MNIUuZcSQlobEg,197
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@@ -70,14 +70,14 @@ dclab/external/skimage/pnpoly.py,sha256=r8hFNiTz5XlUoNZjosqA0iyv1FPn0l7ewbplgFgk
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dclab/external/skimage/_find_contours.py,sha256=16v5eeTZBmevG8SSuXtJ6yUpVPhwfSmtc8pDD0nuuOU,9340
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dclab/external/skimage/__init__.py,sha256=-B2QUKHAFzQuBWuuKvPDC5JIl0Zb-x3OGmbwPaE9VwQ,72
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dclab/external/skimage/_find_contours_cy.cpython-311-darwin.so,sha256=
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dclab/external/skimage/_find_contours_cy.cpython-311-darwin.so,sha256=45z0QOEtuk7P1lk8Xn7BIEajnKZMLeTu1gw4cw_SESE,188824
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dclab/external/skimage/_find_contours_cy.pyx,sha256=pZJOBhMHzYEMkcz4WQVyjn7jDNrdjCfet47FU1hRAxk,7161
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dclab/external/skimage/_pnpoly.cpython-311-darwin.so,sha256=
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dclab/external/skimage/_pnpoly.cpython-311-darwin.so,sha256=BuMZzT4t6dxzl18ucqXQ-4BpgZG3_jZMOmNKF_ylsjQ,207152
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dclab/external/skimage/_shared/geometry.pxd,sha256=kRsu9ifv_rL3kbRIgSLf86p0hn2oTMp6s013lZ9bBZM,346
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dclab/external/skimage/_shared/geometry.cpython-311-darwin.so,sha256=
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dclab/external/skimage/_shared/geometry.cpython-311-darwin.so,sha256=KS6JdkeEQmJbpyu--0S9OQTsp7_jc32eHv-x3qD2oK8,55184
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dclab/external/skimage/_shared/__init__.py,sha256=2sHZwTtJSlMTa3Q2YSvQW7jrPLMUSqDJQa-ROe5zfcw,37
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dclab/external/skimage/_shared/geometry.pyx,sha256=miCHUh6mBDbRRIoaF_0xAER1MRzsCAzFdlYQZhV7RmE,1667
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dclab/definitions/feat_logic.py,sha256=
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dclab/definitions/feat_logic.py,sha256=_Rr2vK-nbRNjxk5Kf8Iohs_Q3jzUe9EZJgxB9vMwxwE,5379
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dclab/definitions/meta_parse.py,sha256=YdaTdM8DAMsIFn5ITH9OHYGTXeAOBGWtx22oVjxXcWk,2393
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dclab/definitions/__init__.py,sha256=56VL7rNTjP61gpGgN2GEUKicds2aBz_nWNwzfNxO_l8,2781
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dclab/definitions/meta_const.py,sha256=zqE-SrD2tJMCFWdtp_IenwnbIQg0lulvbQAw9dK0Gho,13125
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@@ -86,11 +86,11 @@ dclab/definitions/meta_logic.py,sha256=wCgb7DPRHaR8DCWw_VbwNkpslUnazzWfgX0iS8oEe
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dclab/rtdc_dataset/config.py,sha256=MvBteFya3R6Ch3U6UgTakCsJoBgVykTxS_Z25STWPHU,17432
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dclab/rtdc_dataset/check.py,sha256=lJNaz4QTe2WNlxik6zSohRHTiAYuP_bKOzSDjPGTUS0,35006
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dclab/rtdc_dataset/meta_table.py,sha256=ucqBNrgI6rDAuQFuMRckY8lp1LpnYAoRgEsLObWTJCE,648
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dclab/rtdc_dataset/feat_basin.py,sha256=
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dclab/rtdc_dataset/feat_basin.py,sha256=iBGhuRkIy-zbonIjYHCQdLd3V3_cebpBfDTvqyLzJK4,26921
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dclab/rtdc_dataset/fmt_s3.py,sha256=bU3V_WGyqJhxPCH80X_nlNqq-jXcgoZKv_aUBIqwaL8,11877
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dclab/rtdc_dataset/feat_temp.py,sha256=XbDIS1iUUkRH0Zp9uVlwvK_untJ7hkOnKshK1Drsnt8,3694
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dclab/rtdc_dataset/__init__.py,sha256=MUHSGVQJ4Zc0IyU2lf01dpDWyOyNveHip-UjSkmPNvQ,486
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dclab/rtdc_dataset/core.py,sha256=
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dclab/rtdc_dataset/core.py,sha256=LjddGHdqZINXKUQcvCyCDmOofdBzyJIXN_z_C-zWGnM,34777
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dclab/rtdc_dataset/export.py,sha256=Ukmdz-Mm9iei6vhfp1lh7oNQiAbXvA2o3tRx1XlBWCM,33416
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dclab/rtdc_dataset/fmt_dict.py,sha256=gumVQOiVVDFUKow_483PY7cxInqo-NiBBnBhIU8s4lg,3009
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dclab/rtdc_dataset/writer.py,sha256=BqP4QSzHxCSxp9z7_cJF2v04taO3ZXE3Wg6zJY6fMao,41819
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@@ -134,9 +134,9 @@ dclab/rtdc_dataset/fmt_tdms/event_image.py,sha256=-jp7Z-N91e4ieumYQ1huMicj7PMJqw
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dclab/rtdc_dataset/fmt_tdms/event_trace.py,sha256=Vkym0QKSw2mq1XZl5n8wDkgHXmaZwQGiMAV5AuRSJkE,5215
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dclab/rtdc_dataset/fmt_tdms/exc.py,sha256=WzrMqnyrzp8gsT8Pf7JKqGGv43ewx7d_qgtirURppRI,813
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dclab/rtdc_dataset/fmt_tdms/event_contour.py,sha256=kjo0wJx9F0gmmOOyR0NoLw6VEtSl3h63WXXkcbfnoS8,9627
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+
dclab-0.64.2.dist-info/entry_points.txt,sha256=eOpjgznu-eW-9utUpLU-77O5098YyUEgGF3ksGMdtec,273
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dclab-0.64.2.dist-info/top_level.txt,sha256=irvwZMgs1edY1Zj60ZFk7Almb9Zhk4k6E6aC4YPFnnM,6
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dclab-0.64.2.dist-info/METADATA,sha256=AnwRZDfaLbFx0ODuztvp4Yb_ugWo1jrWdCJZl1d5Iwc,4766
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dclab-0.64.2.dist-info/licenses/LICENSE,sha256=gLDaVZWRrlnLdyfOrR0qfWjLbOVcjvoJ-kCLUK0fyXA,15360
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