Multi run select

.github/workflows/ci.yml

@@ -79,7 +79,8 @@ jobs:
       - name: Run PyRS tests
         run: |
           conda activate PyRS
-          xvfb-run --server-args="-screen 0 640x480x24" -a pytest --cov=pyrs --cov-report=xml --cov-report=term tests
+          conda install conda-forge::pytest-xvfb
+          pytest tests
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v1

environment.yml

@@ -1,12 +1,12 @@
 name: PyRS
 channels:
 - conda-forge
-- mantid/label/nightly
+- mantid
 dependencies:
 - python=3.10
 - anaconda-client
 - boa
-- mantidworkbench>=6.8.20231213
+- mantidworkbench>=6.10
 - qtpy
 - pip
 - pyqt=5.15,<6

pyrs/core/peak_profile_utility.py

@@ -6,13 +6,12 @@
 
 
 # Effective peak and background parameters
-EFFECTIVE_PEAK_PARAMETERS = ['Center', 'Height', 'FWHM', 'Mixing', 'A0', 'A1', 'Intensity']
+EFFECTIVE_PEAK_PARAMETERS = ['Center', 'Height', 'FWHM', 'Mixing', 'Intensity', 'A0', 'A1', 'A2']
 
 
 class PeakShape(Enum):
     GAUSSIAN = 'Gaussian'
     PSEUDOVOIGT = 'PseudoVoigt'
-    VOIGT = 'Voigt'
 
     def __str__(self):
         return self.value
@@ -35,14 +34,14 @@ def getShape(shape):
     def native_parameters(self):
         # Native peak parameters in Mantid naming convention
         NATIVE_PEAK_PARAMETERS = {'Gaussian': ['Height', 'PeakCentre', 'Sigma'],
-                                  'PseudoVoigt': ['Mixing', 'Intensity', 'PeakCentre', 'FWHM'],
-                                  'Voigt': ['LorentzAmp', 'LorentzPos', 'LorentzFWHM', 'GaussianFWHM']}
+                                  'PseudoVoigt': ['Mixing', 'Intensity', 'PeakCentre', 'FWHM']}
 
         return NATIVE_PEAK_PARAMETERS[self.value][:]
 
 
 class BackgroundFunction(Enum):
     LINEAR = 'Linear'  # so far, one and only supported
+    QUADRATIC = 'Quadratic'  # so far, one and only supported
 
     def __str__(self):
         return self.value
@@ -64,7 +63,8 @@ def getFunction(function):
     @property
     def native_parameters(self):
         # Native background parameters in Mantid naming convention
-        NATIVE_BACKGROUND_PARAMETERS = {'Linear': ['A0', 'A1']}
+        NATIVE_BACKGROUND_PARAMETERS = {'Linear': ['A0', 'A1'],
+                                        'Quadratic': ['A0', 'A1', 'A2']}
 
         return NATIVE_BACKGROUND_PARAMETERS[self.value][:]
 
@@ -106,8 +106,6 @@ def get_effective_parameters_converter(peak_profile):
         converter = Gaussian()
     elif peak_profile == PeakShape.PSEUDOVOIGT:
         converter = PseudoVoigt()
-    elif peak_profile == PeakShape.VOIGT:
-        converter = Voigt()
     else:
         raise RuntimeError('if/else tree is incomplete')
 
@@ -223,6 +221,13 @@ def calculate_effective_parameters(self, param_value_array, param_error_array):
         eff_error_array['A1'] = param_error_array['A1']  # A1
         eff_error_array['Intensity'] = intensity_error_array[:]  # intensity
 
+        try:
+            eff_value_array['A2'] = param_value_array['A2']  # A2
+            eff_error_array['A2'] = param_error_array['A2']  # A2
+        except ValueError:
+            eff_value_array['A2'] = np.zeros_like(param_value_array['A1'])  # A2
+            eff_error_array['A2'] = np.zeros_like(param_value_array['A1']) + 0.01  # A2
+
         return eff_value_array, eff_error_array
 
     @staticmethod
@@ -396,6 +401,13 @@ def calculate_effective_parameters(self, param_value_array, param_error_array):
         eff_error_array['A1'] = param_error_array['A1']  # A1
         eff_error_array['Intensity'] = param_error_array['Intensity']  # intensity
 
+        try:
+            eff_value_array['A2'] = param_value_array['A2']  # A2
+            eff_error_array['A2'] = param_error_array['A2']  # A2
+        except ValueError:
+            eff_value_array['A2'] = np.zeros_like(param_value_array['A1'])  # A2
+            eff_error_array['A2'] = np.zeros_like(param_value_array['A1']) + 0.01  # A2
+
         return eff_value_array, eff_error_array
 
     @staticmethod
@@ -496,37 +508,6 @@ def cal_intensity(height, fwhm, mixing):
         return intensity
 
 
-class Voigt(PeakParametersConverter):
-    """
-    class for handling peak profile parameters' conversion
-    """
-    def __init__(self):
-        super(Voigt, self).__init__(PeakShape.VOIGT)
-
-    def calculate_effective_parameters(self, param_value_array, param_error_array):
-        """Calculate effective peak parameter values
-
-        If input parameter values include fitting error, then this method will calculate
-        the propagation of error
-
-        Native PseudoVoigt: ['Mixing', 'Intensity', 'PeakCentre', 'FWHM']
-
-        Parameters
-        ----------
-        native_param_names: list or None
-        param_value_array : numpy.ndarray
-            (p, n, 1) or (p, n, 2) vector for parameter values and  optionally fitting error
-            p = number of native parameters , n = number of sub runs
-        param_error_array : numpy.ndarray
-        Returns
-        -------
-        np.ndarray
-            (p', n, 1) or (p', n, 2) array for  parameter values and  optionally fitting error
-            p' = number of effective parameters , n = number of sub runs
-        """
-        raise NotImplementedError('Somebody should write this')
-
-
 """
 From here are a list of static method of peak profiles
 """

pyrs/interface/combine_runs/combine_runs_crtl.py

@@ -0,0 +1,45 @@
+import numpy as np
+from pyrs.utilities import get_input_project_file  # type: ignore
+
+
+class CombineRunsCrtl:
+    def __init__(self, _model):
+        self._model = _model
+
+    def parse_file_path(self, runs):
+        filepaths = []
+        for run in runs:
+            try:
+                filepaths.append(get_input_project_file(int(run)))
+            except FileNotFoundError:
+                pass
+
+        return filepaths
+
+    def parse_entry_list(self, entry_list):
+        entry_list = entry_list.replace(' ', '')
+        split_text = entry_list.split(',')
+        ranges = [entry for entry in split_text if (':' in entry) or (';' in entry)]
+        entries = [entry for entry in split_text if (':' not in entry) and (';' not in entry)]
+
+        runs = np.array([np.int16(entry) for entry in entries])
+        for entry in ranges:
+            split_entry = None
+            if ':' in entry:
+                split_entry = np.array(entry.split(':'), dtype=np.int16)
+            elif ';' in entry:
+                split_entry = np.array(entry.split(';'), dtype=np.int16)
+
+            if split_entry is not None:
+                split_entry = np.sort(split_entry)
+                runs = np.append(runs, np.arange(split_entry[0],
+                                                 split_entry[1]))
+
+        return self.parse_file_path(runs)
+
+    def load_combine_projects(self, project_files):
+        if len(project_files) > 1:
+            self._model.combine_project_files(project_files)
+            return 1
+        else:
+            return 0

pyrs/interface/combine_runs/combine_runs_model.py

@@ -0,0 +1,31 @@
+from qtpy.QtCore import Signal, QObject  # type:ignore
+from pyrs.core.workspaces import HidraWorkspace
+from pyrs.projectfile import HidraProjectFile  # type: ignore
+
+
+class CombineRunsModel(QObject):
+    propertyUpdated = Signal(str)
+    failureMsg = Signal(str, str, str)
+
+    def __init__(self):
+        super().__init__()
+        self._hidra_ws = None
+
+    def combine_project_files(self, project_files):
+        self._hidra_ws = HidraWorkspace('Combined Project Files')
+        _project = HidraProjectFile(project_files[0])
+        self._hidra_ws.load_hidra_project(_project, load_raw_counts=False, load_reduced_diffraction=True)
+        _project.close()
+
+        for project in project_files[1:]:
+            _project = HidraProjectFile(project)
+            self._hidra_ws.append_hidra_project(_project)
+            _project.close()
+
+    def export_project_files(self, fileout):
+        export_project = HidraProjectFile(fileout, 'w')
+        self._hidra_ws.save_experimental_data(export_project,
+                                              sub_runs=self._hidra_ws._sample_logs.subruns,
+                                              ignore_raw_counts=True)
+        self._hidra_ws.save_reduced_diffraction_data(export_project)
+        export_project.save()

pyrs/interface/combine_runs/combine_runs_viewer.py

@@ -0,0 +1,130 @@
+from qtpy.QtWidgets import QHBoxLayout, QLabel, QWidget  # type:ignore
+from qtpy.QtWidgets import QLineEdit, QPushButton  # type:ignore
+from qtpy.QtWidgets import QFileDialog, QGroupBox  # type:ignore
+
+from qtpy.QtWidgets import QGridLayout  # type:ignore
+from qtpy.QtWidgets import QMainWindow  # type:ignore
+from qtpy.QtCore import Qt  # type: ignore
+
+from pyrs.interface.gui_helper import pop_message
+
+
+class FileLoad(QWidget):
+    def __init__(self, name=None, fileType="HidraProjectFile (*.h5);;All Files (*)", parent=None):
+        self._parent = parent
+        super().__init__(parent)
+        self.name = name
+        self.fileType = fileType
+        layout = QHBoxLayout()
+        if name == "Run Numbers:":
+            label = QLabel(name)
+            label.setAlignment(Qt.AlignRight | Qt.AlignVCenter)
+            layout.addWidget(label)
+            self.lineEdit = QLineEdit()
+            self.lineEdit.setReadOnly(False)
+            self.lineEdit.setFixedWidth(300)
+
+            layout.addWidget(self.lineEdit)
+
+            self.browse_button = QPushButton("Load")
+            self.browse_button.clicked.connect(self.loadRunNumbers)
+        else:
+            if name is None:
+                self.browse_button = QPushButton("Browse Exp Data")
+            else:
+                self.browse_button = QPushButton("Browse")
+
+            self.browse_button.clicked.connect(self.openFileDialog)
+
+        layout.addWidget(self.browse_button)
+        self.setLayout(layout)
+
+    def _reset_fit_data(self):
+        self._parent.fit_summary.fit_table_operator.fits = None
+        self._parent.fit_summary.fit_table_operator.fit_result = None
+
+    def openFileDialog(self):
+        self._parent._project_files, _ = QFileDialog.getOpenFileNames(self,
+                                                                      self.name,
+                                                                      "",
+                                                                      self.fileType,
+                                                                      options=QFileDialog.DontUseNativeDialog)
+
+        if self._parent._project_files:
+            self._parent.load_project_files = self._parent._project_files
+
+            self.load_project_files()
+
+    def saveFileDialog(self, combined_files):
+        if combined_files != 0:
+            self._parent._project_files, _ = QFileDialog.getSaveFileName(self,
+                                                                         'Save Combined Proeject File',
+                                                                         "",
+                                                                         self.fileType,
+                                                                         options=QFileDialog.DontUseNativeDialog)
+
+    def loadRunNumbers(self):
+        self._parent._project_files = self._parent.controller.parse_entry_list(self.lineEdit.text())
+        combined_files = self._parent.controller.load_combine_projects(self._parent._project_files)
+        self.saveFileDialog(combined_files)
+
+    def load_project_files(self):
+        try:
+            combined_files = self._parent.controller.load_combine_projects(self._parent._project_files)
+            self.saveFileDialog(combined_files)
+
+        except (FileNotFoundError, RuntimeError, ValueError) as run_err:
+            pop_message(self, f'Failed to find run {self._parent._project_files}',
+                        str(run_err), 'error')
+
+            self._parent.load_project_files = None
+
+    def setFilenamesText(self, filenames):
+        self.lineEdit.setText(filenames)
+
+
+class FileLoading(QGroupBox):
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.setTitle("Load Project Files")
+        layout = QHBoxLayout()
+
+        self.file_load_run_number = FileLoad(name="Run Numbers:", parent=parent)
+        self.file_load_dilg = FileLoad(name=None, parent=parent)
+
+        layout.addWidget(self.file_load_run_number)
+        layout.addWidget(self.file_load_dilg)
+
+        self.setLayout(layout)
+
+    def set_text_values(self, direction, text):
+        getattr(self, f"file_load_e{direction}").setFilenamesText(text)
+
+
+class CombineRunsViewer(QMainWindow):
+    def __init__(self, combine_runs_model, combine_runs_ctrl, parent=None):
+
+        self._model = combine_runs_model
+        self._ctrl = combine_runs_ctrl
+        self._nexus_file = None
+        self._run_number = None
+        self._calibration_input = None
+
+        super().__init__(parent)
+
+        self.setWindowTitle("PyRS Combine Projectfiles Window")
+
+        self.fileLoading = FileLoading(self)
+
+        self.window = QWidget()
+        self.layout = QGridLayout()
+        self.setCentralWidget(self.fileLoading)
+        self.window.setLayout(self.layout)
+
+    @property
+    def controller(self):
+        return self._ctrl
+
+    @property
+    def model(self):
+        return self._model

pyrs/interface/designer/peakfitwindow.ui

@@ -398,11 +398,6 @@
                     <string>Gaussian</string>
                    </property>
                   </item>
-                  <item>
-                   <property name="text">
-                    <string>Voigt</string>
-                   </property>
-                  </item>
                  </widget>
                 </item>
                 <item>
@@ -412,11 +407,6 @@
                     <string>Linear</string>
                    </property>
                   </item>
-                  <item>
-                   <property name="text">
-                    <string>Flat</string>
-                   </property>
-                  </item>
                   <item>
                    <property name="text">
                     <string>Quadratic</string>
@@ -942,7 +932,7 @@
      <x>0</x>
      <y>0</y>
      <width>1536</width>
-     <height>23</height>
+     <height>22</height>
     </rect>
    </property>
    <widget class="QMenu" name="menuFile">