dcscope 2.22.1__py3-none-any.whl

dcscope/gui/bulk/bulk_emodulus.ui

@@ -0,0 +1,245 @@
+<?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>400</width>
+    <height>274</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Young's modulus computation</string>
+  </property>
+  <property name="windowIcon">
+   <iconset theme="view-statistics"/>
+  </property>
+  <layout class="QVBoxLayout" name="verticalLayout">
+   <item>
+    <widget class="QLabel" name="label">
+     <property name="text">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Here you can set the parameters for Young's modulus computation for all datasets loaded. This is the bulk-version of the corresponding options in the &lt;span style=&quot; font-style:italic;&quot;&gt;Dataset  &lt;/span&gt; tab in the &lt;span style=&quot; font-style:italic;&quot;&gt;Analysis View&lt;/span&gt;.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="wordWrap">
+      <bool>true</bool>
+     </property>
+    </widget>
+   </item>
+   <item>
+    <layout class="QGridLayout" name="gridLayout">
+     <item row="1" column="2">
+      <widget class="DoubleSpinBoxNan" name="doubleSpinBox_temp">
+       <property name="wrapping">
+        <bool>false</bool>
+       </property>
+       <property name="readOnly">
+        <bool>false</bool>
+       </property>
+       <property name="specialValueText">
+        <string/>
+       </property>
+       <property name="suffix">
+        <string>°C</string>
+       </property>
+       <property name="minimum">
+        <double>10.000000000000000</double>
+       </property>
+       <property name="maximum">
+        <double>45.000000000000000</double>
+       </property>
+       <property name="value">
+        <double>23.000000000000000</double>
+       </property>
+      </widget>
+     </item>
+     <item row="0" column="1">
+      <widget class="QComboBox" name="comboBox_medium">
+       <property name="currentIndex">
+        <number>0</number>
+       </property>
+       <item>
+        <property name="text">
+         <string>CellCarrier</string>
+        </property>
+       </item>
+       <item>
+        <property name="text">
+         <string>CellCarrier B</string>
+        </property>
+       </item>
+       <item>
+        <property name="text">
+         <string>water</string>
+        </property>
+       </item>
+       <item>
+        <property name="text">
+         <string>other</string>
+        </property>
+       </item>
+       <item>
+        <property name="text">
+         <string>unknown</string>
+        </property>
+       </item>
+      </widget>
+     </item>
+     <item row="0" column="0">
+      <widget class="QLabel" name="label_6">
+       <property name="text">
+        <string>Medium</string>
+       </property>
+      </widget>
+     </item>
+     <item row="1" column="3">
+      <spacer name="horizontalSpacer">
+       <property name="orientation">
+        <enum>Qt::Orientation::Horizontal</enum>
+       </property>
+       <property name="sizeHint" stdset="0">
+        <size>
+         <width>0</width>
+         <height>20</height>
+        </size>
+       </property>
+      </spacer>
+     </item>
+     <item row="2" column="1">
+      <widget class="QComboBox" name="comboBox_visc_model">
+       <item>
+        <property name="text">
+         <string>buyukurganci-2022</string>
+        </property>
+       </item>
+       <item>
+        <property name="text">
+         <string>herold-2017</string>
+        </property>
+       </item>
+      </widget>
+     </item>
+     <item row="1" column="1">
+      <widget class="QComboBox" name="comboBox_temp">
+       <item>
+        <property name="text">
+         <string>Configuration</string>
+        </property>
+       </item>
+       <item>
+        <property name="text">
+         <string>Feature</string>
+        </property>
+       </item>
+       <item>
+        <property name="text">
+         <string>Manual</string>
+        </property>
+       </item>
+      </widget>
+     </item>
+     <item row="2" column="0">
+      <widget class="QLabel" name="label_8">
+       <property name="text">
+        <string>Viscosity</string>
+       </property>
+      </widget>
+     </item>
+     <item row="1" column="0">
+      <widget class="QLabel" name="label_temp">
+       <property name="text">
+        <string>Temperature</string>
+       </property>
+      </widget>
+     </item>
+     <item row="2" column="2">
+      <widget class="DoubleSpinBoxNan" name="doubleSpinBox_visc">
+       <property name="showGroupSeparator" stdset="0">
+        <bool>false</bool>
+       </property>
+       <property name="suffix">
+        <string> mPa·s</string>
+       </property>
+      </widget>
+     </item>
+     <item row="3" column="0">
+      <widget class="QLabel" name="label_2">
+       <property name="text">
+        <string>Look-up table</string>
+       </property>
+      </widget>
+     </item>
+     <item row="3" column="1">
+      <widget class="QComboBox" name="comboBox_lut"/>
+     </item>
+    </layout>
+   </item>
+   <item>
+    <spacer name="verticalSpacer">
+     <property name="orientation">
+      <enum>Qt::Orientation::Vertical</enum>
+     </property>
+     <property name="sizeHint" stdset="0">
+      <size>
+       <width>20</width>
+       <height>0</height>
+      </size>
+     </property>
+    </spacer>
+   </item>
+   <item>
+    <widget class="QDialogButtonBox" name="buttonBox">
+     <property name="orientation">
+      <enum>Qt::Orientation::Horizontal</enum>
+     </property>
+     <property name="standardButtons">
+      <set>QDialogButtonBox::StandardButton::Cancel|QDialogButtonBox::StandardButton::Ok</set>
+     </property>
+    </widget>
+   </item>
+  </layout>
+ </widget>
+ <customwidgets>
+  <customwidget>
+   <class>DoubleSpinBoxNan</class>
+   <extends>QDoubleSpinBox</extends>
+   <header>dcscope.gui.widgets</header>
+  </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>

dcscope/gui/compute/__init__.py

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+# flake8: noqa: F401
+from .comp_lme4 import ComputeSignificance
+from .comp_stats import ComputeStatistics

dcscope/gui/compute/comp_lme4.py

@@ -0,0 +1,115 @@
+import importlib.resources
+import webbrowser
+
+from dclab import lme4
+from PyQt6 import uic, QtCore, QtGui, QtWidgets
+
+from .comp_lme4_dataset import LME4Dataset
+from .comp_lme4_results import Rlme4ResultsDialog
+
+from ..widgets import ShowWaitCursor
+
+
+class ComputeSignificance(QtWidgets.QDialog):
+    def __init__(self, parent, pipeline, *args, **kwargs):
+        super(ComputeSignificance, self).__init__(parent, *args, **kwargs)
+        ref = importlib.resources.files(
+            "dcscope.gui.compute") / "comp_lme4.ui"
+        with importlib.resources.as_file(ref) as path_ui:
+            uic.loadUi(path_ui, self)
+
+        # set pipeline
+        self.pipeline = pipeline
+
+        # populate feature combo box
+        feats, labs = pipeline.get_features(scalar=True, label_sort=True,
+                                            union=False, ret_labels=True)
+        for feat, lab in zip(feats, labs):
+            self.comboBox_feat.addItem(lab, feat)
+
+        # populate datasets
+        self.datasets = []
+        for slot in self.pipeline.slots:
+            dw = LME4Dataset(self, slot=slot)
+            self.dataset_layout.addWidget(dw)
+            self.datasets.append(dw)
+        spacer = QtWidgets.QSpacerItem(20, 0,
+                                       QtWidgets.QSizePolicy.Policy.Minimum,
+                                       QtWidgets.QSizePolicy.Policy.Expanding)
+        self.dataset_layout.addItem(spacer)
+        self.update()
+
+        # button signals
+        btn_close = self.buttonBox.button(
+            QtWidgets.QDialogButtonBox.StandardButton.Close)
+        btn_close.clicked.connect(self.on_close)
+        btn_close.setToolTip("Close this dialog")
+        closeicon = QtGui.QIcon.fromTheme("dialog-close")
+        btn_close.setIcon(closeicon)
+        btn_openlme4 = self.buttonBox.button(
+            QtWidgets.QDialogButtonBox.StandardButton.Apply)
+        btn_openlme4.clicked.connect(self.on_lme4)
+        btn_openlme4.setToolTip("Perform lme4 analysis")
+        btn_openlme4.setText("Run R-lme4")
+        picon = QtGui.QIcon.fromTheme("rlang")
+        btn_openlme4.setIcon(picon)
+        btn_help = self.buttonBox.button(
+            QtWidgets.QDialogButtonBox.StandardButton.Help)
+        btn_help.clicked.connect(self.on_help)
+        btn_help.setToolTip("View R-lme4 Quick Guide online")
+        helpicon = QtGui.QIcon.fromTheme("documentinfo")
+        btn_help.setIcon(helpicon)
+
+    @property
+    def feature(self):
+        return self.comboBox_feat.currentData()
+
+    @property
+    def model(self):
+        if self.radioButton_lmer.isChecked():
+            return "lmer"
+        else:
+            return "glmer+loglink"
+
+    @QtCore.pyqtSlot()
+    def on_lme4(self, ret_dlg=False):
+        """Run lme4 analysis
+
+        Parameters
+        ----------
+        ret_dlg: bool
+            If set to True, then the dialog is returned without
+            `_exec`uting it (used for testing).
+        """
+        self.setEnabled(False)
+        # set R HOME from settings
+        settings = QtCore.QSettings()
+        r_path = settings.value("lme4/r path", "")
+        if r_path:
+            lme4.set_r_path(r_path)
+        r_libs_path = settings.value("lme4/r libs user", "")
+        if r_libs_path:
+            lme4.set_r_lib_path(r_libs_path)
+        # compute LMM
+        with ShowWaitCursor():
+            rlme4 = lme4.Rlme4(model=self.model, feature=self.feature)
+            for wds in self.datasets:
+                wds.add_to_rlme4(self.pipeline, rlme4)
+            result = rlme4.fit()
+        self.setEnabled(True)
+        dlg = Rlme4ResultsDialog(self, result)
+        if ret_dlg:
+            return dlg
+        else:
+            dlg.exec()
+
+    @QtCore.pyqtSlot()
+    def on_close(self):
+        """Close window"""
+        self.close()
+
+    @QtCore.pyqtSlot()
+    def on_help(self):
+        """Show DCscope docs"""
+        webbrowser.open(
+            "https://dclab.readthedocs.io/en/stable/sec_av_lme4.html")

dcscope/gui/compute/comp_lme4.ui

@@ -0,0 +1,194 @@
+<?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>593</width>
+    <height>544</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Compute statistical significance with R-lme4</string>
+  </property>
+  <property name="windowIcon">
+   <iconset theme="statistical_significance">
+    <normaloff>../../../../../.designer/backup</normaloff>../../../../../.designer/backup</iconset>
+  </property>
+  <layout class="QVBoxLayout" name="verticalLayout_3">
+   <item>
+    <widget class="QLabel" name="label">
+     <property name="text">
+      <string>Compute the statistical significance using linear mixed-effects models</string>
+     </property>
+    </widget>
+   </item>
+   <item>
+    <layout class="QHBoxLayout" name="horizontalLayout_2">
+     <item>
+      <widget class="QLabel" name="label_2">
+       <property name="text">
+        <string>Model:</string>
+       </property>
+      </widget>
+     </item>
+     <item>
+      <widget class="QRadioButton" name="radioButton_lmer">
+       <property name="toolTip">
+        <string>linear mixed-effects model</string>
+       </property>
+       <property name="text">
+        <string>lmer</string>
+       </property>
+       <property name="checked">
+        <bool>true</bool>
+       </property>
+      </widget>
+     </item>
+     <item>
+      <widget class="QRadioButton" name="radioButton_glmer">
+       <property name="toolTip">
+        <string>generalized linear mixed-effects model with a log-link function</string>
+       </property>
+       <property name="text">
+        <string>glmer+loglink</string>
+       </property>
+      </widget>
+     </item>
+     <item>
+      <spacer name="horizontalSpacer">
+       <property name="orientation">
+        <enum>Qt::Horizontal</enum>
+       </property>
+       <property name="sizeHint" stdset="0">
+        <size>
+         <width>40</width>
+         <height>20</height>
+        </size>
+       </property>
+      </spacer>
+     </item>
+    </layout>
+   </item>
+   <item>
+    <layout class="QHBoxLayout" name="horizontalLayout_3">
+     <item>
+      <widget class="QLabel" name="label_3">
+       <property name="text">
+        <string>Feature:</string>
+       </property>
+      </widget>
+     </item>
+     <item>
+      <widget class="QComboBox" name="comboBox_feat">
+       <property name="sizePolicy">
+        <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+         <horstretch>0</horstretch>
+         <verstretch>0</verstretch>
+        </sizepolicy>
+       </property>
+      </widget>
+     </item>
+     <item>
+      <spacer name="horizontalSpacer_2">
+       <property name="orientation">
+        <enum>Qt::Horizontal</enum>
+       </property>
+       <property name="sizeHint" stdset="0">
+        <size>
+         <width>40</width>
+         <height>20</height>
+        </size>
+       </property>
+      </spacer>
+     </item>
+    </layout>
+   </item>
+   <item>
+    <widget class="QLabel" name="label_4">
+     <property name="text">
+      <string>Datasets:</string>
+     </property>
+    </widget>
+   </item>
+   <item>
+    <widget class="QScrollArea" name="scrollArea">
+     <property name="horizontalScrollBarPolicy">
+      <enum>Qt::ScrollBarAlwaysOff</enum>
+     </property>
+     <property name="sizeAdjustPolicy">
+      <enum>QAbstractScrollArea::AdjustToContents</enum>
+     </property>
+     <property name="widgetResizable">
+      <bool>true</bool>
+     </property>
+     <widget class="QWidget" name="scrollAreaWidgetContents">
+      <property name="geometry">
+       <rect>
+        <x>0</x>
+        <y>0</y>
+        <width>573</width>
+        <height>396</height>
+       </rect>
+      </property>
+      <layout class="QVBoxLayout" name="verticalLayout_4">
+       <item>
+        <layout class="QVBoxLayout" name="dataset_layout"/>
+       </item>
+      </layout>
+     </widget>
+    </widget>
+   </item>
+   <item>
+    <widget class="QDialogButtonBox" name="buttonBox">
+     <property name="orientation">
+      <enum>Qt::Horizontal</enum>
+     </property>
+     <property name="standardButtons">
+      <set>QDialogButtonBox::Apply|QDialogButtonBox::Close|QDialogButtonBox::Help</set>
+     </property>
+     <property name="centerButtons">
+      <bool>false</bool>
+     </property>
+    </widget>
+   </item>
+  </layout>
+ </widget>
+ <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>

dcscope/gui/compute/comp_lme4_dataset.py

@@ -0,0 +1,51 @@
+import importlib.resources
+
+from PyQt6 import uic, QtGui, QtWidgets
+
+from ... import meta_tool
+
+
+class LME4Dataset(QtWidgets.QDialog):
+    def __init__(self, parent, slot, *args, **kwargs):
+        super(LME4Dataset, self).__init__(parent, *args, **kwargs)
+        ref = importlib.resources.files(
+            "dcscope.gui.compute") / "comp_lme4_dataset.ui"
+        with importlib.resources.as_file(ref) as path_ui:
+            uic.loadUi(path_ui, self)
+
+        self.identifier = slot.identifier
+
+        # set dataset label
+        self.checkBox_dataset.setText(slot.name)
+
+        # set region icon
+        region = meta_tool.get_info(slot.path,
+                                    section="setup",
+                                    key="chip region")
+        icon = QtGui.QIcon.fromTheme("region_{}".format(region))
+        pixmap = icon.pixmap(16)
+        self.label_region.setPixmap(pixmap)
+        self.label_region.setToolTip(region)
+
+    def add_to_rlme4(self, pipeline, rlme4):
+        """Add the dataset to an Rlme4 analysis
+
+        Parameters
+        ----------
+        pipeline: dcscope.pipeline.core.Pipeline
+            The pipeline from which to extract the filtered dataset
+            using `self.identifier`.
+        rlme4: dclab.lme4.wrapr.Rlme4
+            The analysis to which to append this dataset.
+
+        Notes
+        -----
+        If the check box is not checked, then the dataset is ignored.
+        """
+        if self.checkBox_dataset.isChecked():
+            ds_index = pipeline.slot_ids.index(self.identifier)
+            ds = pipeline.get_dataset(ds_index)
+            group_id = self.comboBox_group.currentIndex()
+            group = "control" if group_id == 0 else "treatment"
+            repetition = self.spinBox_repeat.value()
+            rlme4.add_dataset(ds=ds, group=group, repetition=repetition)