dcscope 2.22.1__py3-none-any.whl

dcscope/gui/compute/comp_stats.py

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+import codecs
+import numbers
+import pathlib
+import importlib.resources
+import time
+
+import dclab
+from PyQt6 import uic, QtCore, QtWidgets
+
+from ..widgets import show_wait_cursor
+from ..widgets.feature_combobox import HIDDEN_FEATURES
+from ..._version import version
+
+STAT_METHODS = sorted(dclab.statistics.Statistics.available_methods.keys())
+STAT_METHODS.remove("%-gated")  # This does not make sense with Pipeline
+
+
+class ComputeStatistics(QtWidgets.QDialog):
+    def __init__(self, parent, pipeline, *args, **kwargs):
+        super(ComputeStatistics, self).__init__(parent=parent, *args, **kwargs)
+        ref = importlib.resources.files(
+            "dcscope.gui.compute") / "comp_stats.ui"
+        with importlib.resources.as_file(ref) as path_ui:
+            uic.loadUi(path_ui, self)
+
+        # for external statistics
+        self.path = None
+        # set pipeline
+        self.pipeline = pipeline
+        # Signals
+        self.pushButton_path.clicked.connect(self.on_browse)
+        self.comboBox.currentIndexChanged.connect(self.on_combobox)
+        # Populate statistics methods
+        self.bulklist_stats.set_title("Statistical methods")
+        self.bulklist_stats.set_items(STAT_METHODS)
+        self.bulklist_stats.on_select_all()
+        # Populate filter ray comboBox
+        self.comboBox_filter_ray.clear()
+        self.comboBox_filter_ray.addItem("No filtering", None)
+        for ii, slot in enumerate(pipeline.slots):
+            if slot.slot_used:
+                raytext = "Ray {} ({})".format(ii, slot.name)
+                self.comboBox_filter_ray.addItem(raytext, slot.identifier)
+        # initialize feature list
+        self.bulklist_features.set_title("Features")
+        # initialize rest
+        if len(self.pipeline.slots) == 0:
+            self.comboBox.setCurrentIndex(1)
+        else:
+            self.comboBox.setCurrentIndex(0)
+        self.on_combobox()  # computes self.features
+        # Only select innate features
+        self.on_select_features_innate()
+
+    def done(self, r):
+        if r:
+            success = self.export_statistics()
+        else:
+            success = True
+        if success:
+            super(ComputeStatistics, self).done(r)
+
+    @show_wait_cursor
+    @QtCore.pyqtSlot()
+    def export_statistics(self):
+        """Export statistics to .tsv"""
+        # Output path
+        opath, _ = QtWidgets.QFileDialog.getSaveFileName(
+            self, 'Save statistics', '', 'tab-separated values (*.tsv)')
+        if not opath:
+            # Abort export
+            return False
+        elif not opath.endswith(".tsv"):
+            opath += ".tsv"
+        opath = pathlib.Path(opath)
+
+        # get features
+        features = self.bulklist_features.get_selection()
+        # get methods
+        methods = self.bulklist_stats.get_selection()
+        prog = QtWidgets.QProgressDialog("Computing statistics...", "Abort", 1,
+                                         1, self)
+        prog.setMinimumDuration(0)
+        time.sleep(0.01)
+        prog.setValue(0)
+        # compute statistics
+        values = []
+        if self.comboBox.currentIndex() == 0:
+            # from pipeline
+            prog.setMaximum(len(self.pipeline.slots))
+            for slot_index in range(len(self.pipeline.slots)):
+                slot = self.pipeline.slots[slot_index]
+                if slot.slot_used:  # only export slots "used" (#15)
+                    ds = self.pipeline.get_dataset(slot_index)
+                    h, v = dclab.statistics.get_statistics(ds,
+                                                           methods=methods,
+                                                           features=features)
+                    h = ["Path", "Slot", "Name"] + h
+                    v = ["{}".format(ds.path), slot_index, slot.name] + v
+                    values.append(v)
+                if prog.wasCanceled():
+                    break
+                prog.setValue(slot_index + 1)
+                QtWidgets.QApplication.processEvents(
+                    QtCore.QEventLoop.ProcessEventsFlag.AllEvents, 300)
+        else:
+            # from path
+            inpath = pathlib.Path(self.path)
+            files = sorted(inpath.rglob("*.rtdc"))
+            prog.setMaximum(len(files))
+            for ii, pp in enumerate(files):
+                ds = dclab.new_dataset(pp)
+                title = ds.title
+                slot_id = self.comboBox_filter_ray.currentData()
+                if slot_id is not None:
+                    ds = self.pipeline.apply_filter_ray(rtdc_ds=ds,
+                                                        slot_id=slot_id)
+                    title += " ({})".format(slot_id)
+                h, v = dclab.statistics.get_statistics(ds,
+                                                       methods=methods,
+                                                       features=features)
+                h = ["Path", "Name"] + h
+                v = ["{}".format(pp), title] + v
+                values.append(v)
+                prog.setValue(ii + 1)
+                QtWidgets.QApplication.processEvents(
+                    QtCore.QEventLoop.ProcessEventsFlag.AllEvents, 300)
+
+        # Header
+        header = ["Statistics Output",
+                  "DCscope {}".format(version),
+                  "",
+                  "\t".join(h),
+                  ]
+        # Data
+        data = []
+        for v in values:
+            line = []
+            for vi in v:
+                if (isinstance(vi, numbers.Real)
+                        and not isinstance(vi, numbers.Integral)):
+                    line.append("{:.5e}".format(vi))
+                else:
+                    line.append("{}".format(vi))
+            data.append("\t".join(line))
+        # Write BOM
+        with opath.open("wb") as fd:
+            fd.write(codecs.BOM_UTF8)
+        # Write rest
+        with opath.open("a", encoding="utf-8") as fd:
+            for line in header:
+                fd.write("# " + line + "\n")
+            for line in data:
+                fd.write(line + "\n")
+        return True  # True means success
+
+    @QtCore.pyqtSlot()
+    def on_browse(self):
+        out = QtWidgets.QFileDialog.getExistingDirectory(self,
+                                                         'Export directory')
+        if out:
+            self.path = out
+            self.lineEdit_path.setText(self.path)
+            self.comboBox.setCurrentIndex(1)
+        else:
+            self.path = None
+            self.comboBox.setCurrentIndex(0)
+
+    @QtCore.pyqtSlot()
+    def on_combobox(self):
+        if self.comboBox.currentIndex() == 1:
+            # Datasets from a folder
+            self.widget_other.show()
+            if self.path is None:
+                self.on_browse()
+            if self.path:
+                self.update_feature_list(use_pipeline=False)
+                # else, on_combobox is triggered again
+        else:
+            # Datasets from current session
+            self.widget_other.hide()
+            self.update_feature_list(use_pipeline=True)
+
+    @QtCore.pyqtSlot()
+    def on_select_features_innate(self):
+        """Only select all innate features of the first dataset"""
+
+        if self.pipeline.num_slots:
+            ds = self.pipeline.get_dataset(0)
+            features_innate = ds.features_innate
+            lw = self.bulklist_features.listWidget
+            for ii in range(lw.count()):
+                wid = lw.item(ii)
+                for feat in features_innate:
+                    if wid.data(101) == feat:
+                        wid.setCheckState(QtCore.Qt.CheckState.Checked)
+                        break
+                else:
+                    wid.setCheckState(QtCore.Qt.CheckState.Unchecked)
+
+    def update_feature_list(self, use_pipeline=True):
+        if use_pipeline:
+            self.features = self.pipeline.get_features(scalar=True,
+                                                       union=True,
+                                                       label_sort=True)
+        else:
+            # We want to compute statistics from a folder
+            # TODO:
+            # - Add ml_score_??? features
+
+            # label-sorted features
+            features = dclab.dfn.scalar_feature_names
+            labs = [dclab.dfn.get_feature_label(f) for f in features]
+            lf = sorted(zip(labs, features))
+            self.features = [it[1] for it in lf]
+
+        # do not compute statistics for basinmap features
+        for feat in HIDDEN_FEATURES + ["index"]:
+            if feat in self.features:
+                self.features.remove(feat)
+
+        labels = [dclab.dfn.get_feature_label(feat) for feat in self.features]
+        self.bulklist_features.set_items(self.features, labels)

dcscope/gui/compute/comp_stats.ui

@@ -0,0 +1,187 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>Dialog</class>
+ <widget class="QDialog" name="Dialog">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>693</width>
+    <height>446</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Compute and export statistical data</string>
+  </property>
+  <property name="windowIcon">
+   <iconset theme="view-statistics">
+    <normaloff>.</normaloff>.</iconset>
+  </property>
+  <layout class="QVBoxLayout" name="verticalLayout">
+   <item>
+    <widget class="QLabel" name="label">
+     <property name="text">
+      <string>Compute statistics for multiple datasets.</string>
+     </property>
+    </widget>
+   </item>
+   <item>
+    <widget class="QComboBox" name="comboBox">
+     <item>
+      <property name="text">
+       <string>All datasets of the current session</string>
+      </property>
+     </item>
+     <item>
+      <property name="text">
+       <string>All datasets in a directory</string>
+      </property>
+     </item>
+    </widget>
+   </item>
+   <item>
+    <widget class="QWidget" name="widget_other" native="true">
+     <layout class="QVBoxLayout" name="verticalLayout_2">
+      <property name="leftMargin">
+       <number>0</number>
+      </property>
+      <property name="topMargin">
+       <number>0</number>
+      </property>
+      <property name="rightMargin">
+       <number>0</number>
+      </property>
+      <property name="bottomMargin">
+       <number>0</number>
+      </property>
+      <item>
+       <layout class="QHBoxLayout" name="horizontalLayout_3">
+        <property name="topMargin">
+         <number>0</number>
+        </property>
+        <item>
+         <widget class="QLineEdit" name="lineEdit_path">
+          <property name="placeholderText">
+           <string>PATH</string>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <widget class="QPushButton" name="pushButton_path">
+          <property name="text">
+           <string>Browse</string>
+          </property>
+         </widget>
+        </item>
+       </layout>
+      </item>
+      <item>
+       <layout class="QHBoxLayout" name="horizontalLayout_4">
+        <property name="topMargin">
+         <number>0</number>
+        </property>
+        <item>
+         <widget class="QLabel" name="label_2">
+          <property name="toolTip">
+           <string>All filters from this filter ray will be applied before computing statistics</string>
+          </property>
+          <property name="text">
+           <string>Filter ray</string>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <widget class="QComboBox" name="comboBox_filter_ray">
+          <property name="sizePolicy">
+           <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+            <horstretch>0</horstretch>
+            <verstretch>0</verstretch>
+           </sizepolicy>
+          </property>
+         </widget>
+        </item>
+       </layout>
+      </item>
+     </layout>
+    </widget>
+   </item>
+   <item>
+    <layout class="QHBoxLayout" name="horizontalLayout_2" stretch="2,1">
+     <item>
+      <widget class="BulkList" name="bulklist_features" native="true">
+       <property name="sizePolicy">
+        <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
+         <horstretch>0</horstretch>
+         <verstretch>0</verstretch>
+        </sizepolicy>
+       </property>
+      </widget>
+     </item>
+     <item>
+      <widget class="BulkList" name="bulklist_stats" native="true">
+       <property name="sizePolicy">
+        <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
+         <horstretch>0</horstretch>
+         <verstretch>0</verstretch>
+        </sizepolicy>
+       </property>
+      </widget>
+     </item>
+    </layout>
+   </item>
+   <item>
+    <widget class="QDialogButtonBox" name="buttonBox">
+     <property name="orientation">
+      <enum>Qt::Horizontal</enum>
+     </property>
+     <property name="standardButtons">
+      <set>QDialogButtonBox::Cancel|QDialogButtonBox::Ok</set>
+     </property>
+    </widget>
+   </item>
+  </layout>
+ </widget>
+ <customwidgets>
+  <customwidget>
+   <class>BulkList</class>
+   <extends>QWidget</extends>
+   <header>dcscope.gui.widgets.bulk_list</header>
+   <container>1</container>
+  </customwidget>
+ </customwidgets>
+ <resources/>
+ <connections>
+  <connection>
+   <sender>buttonBox</sender>
+   <signal>accepted()</signal>
+   <receiver>Dialog</receiver>
+   <slot>accept()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>248</x>
+     <y>254</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>157</x>
+     <y>274</y>
+    </hint>
+   </hints>
+  </connection>
+  <connection>
+   <sender>buttonBox</sender>
+   <signal>rejected()</signal>
+   <receiver>Dialog</receiver>
+   <slot>reject()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>316</x>
+     <y>260</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>286</x>
+     <y>274</y>
+    </hint>
+   </hints>
+  </connection>
+ </connections>
+</ui>