Merge pull request #240 from zhujun98/peak_finding_for_azimuthal_integration

Implement peak finding in Azimuthal Integration View.

Author: zhujun98

extra_foam/algorithms/__init__.py

@@ -42,4 +42,8 @@
 
 from .computer_vision import (
     edge_detect, fourier_transform_2d
-)
+)
+
+from .peak_finding import (
+    find_peaks_1d
+)

extra_foam/algorithms/peak_finding.py

@@ -0,0 +1,14 @@
+"""
+Distributed under the terms of the BSD 3-Clause License.
+
+The full license is in the file LICENSE, distributed with this software.
+
+Author: Jun Zhu <[email protected]>
+Copyright (C) European X-Ray Free-Electron Laser Facility GmbH.
+All rights reserved.
+"""
+from scipy.signal import find_peaks
+
+
+def find_peaks_1d(a, *args, **kwargs):
+    return find_peaks(a, *args, **kwargs)

extra_foam/gui/ctrl_widgets/azimuthal_integ_ctrl_widget.py

@@ -11,16 +11,21 @@
 
 from PyQt5.QtCore import Qt
 from PyQt5.QtGui import QDoubleValidator, QIntValidator
-from PyQt5.QtWidgets import QComboBox, QGridLayout, QLabel
+from PyQt5.QtWidgets import (
+    QCheckBox, QComboBox, QFrame, QGridLayout, QHBoxLayout, QLabel
+)
 
 from .base_ctrl_widgets import _AbstractCtrlWidget
-from .smart_widgets import SmartBoundaryLineEdit, SmartLineEdit
+from .smart_widgets import (
+    SmartBoundaryLineEdit, SmartSliceLineEdit, SmartLineEdit
+)
 from ..gui_helpers import invert_dict
 from ...algorithms import compute_q
 from ...config import config, list_azimuthal_integ_methods, Normalizer
 from ...database import Metadata as mt
 
 _DEFAULT_AZIMUTHAL_INTEG_POINTS = 512
+_DEFAULT_PEAK_PROMINENCE = 100
 
 
 def _estimate_q_range():
@@ -90,56 +95,85 @@ def __init__(self, *args, **kwargs):
         self._auc_range_le = SmartBoundaryLineEdit("0, Inf")
         self._fom_integ_range_le = SmartBoundaryLineEdit("0, Inf")
 
+        self._peak_finding_cb = QCheckBox("Peak finding")
+        self._peak_finding_cb.setChecked(True)
+        self._peak_prominence_le = SmartLineEdit(str(_DEFAULT_PEAK_PROMINENCE))
+        self._peak_prominence_le.setValidator(QIntValidator())
+        self._peak_slicer_le = SmartSliceLineEdit(":")
+
+        self._non_reconfigurable_widgets = [
+        ]
+
         self.initUI()
         self.initConnections()
 
         self.setFixedHeight(self.minimumSizeHint().height())
 
     def initUI(self):
         """Override."""
-        layout = QGridLayout()
+        layout = QHBoxLayout()
         AR = Qt.AlignRight
 
+        param_widget = QFrame()
+        param_layout = QGridLayout()
         row = 0
-        layout.addWidget(QLabel("Cx (pixel): "), row, 0, AR)
-        layout.addWidget(self._cx_le, row, 1)
-        layout.addWidget(QLabel("Cy (pixel): "), row, 2, AR)
-        layout.addWidget(self._cy_le, row, 3)
-        layout.addWidget(QLabel("Pixel x (m): "), row, 4, AR)
-        layout.addWidget(self._px_le, row, 5)
-        layout.addWidget(QLabel("Pixel y (m): "), row, 6, AR)
-        layout.addWidget(self._py_le, row, 7)
+        param_layout.addWidget(QLabel("Cx (pixel): "), row, 0, AR)
+        param_layout.addWidget(self._cx_le, row, 1)
+        param_layout.addWidget(QLabel("Cy (pixel): "), row, 2, AR)
+        param_layout.addWidget(self._cy_le, row, 3)
+        param_layout.addWidget(QLabel("Pixel x (m): "), row, 4, AR)
+        param_layout.addWidget(self._px_le, row, 5)
+        param_layout.addWidget(QLabel("Pixel y (m): "), row, 6, AR)
+        param_layout.addWidget(self._py_le, row, 7)
 
         row += 1
-        layout.addWidget(QLabel("Sample distance (m): "), row, 0, AR)
-        layout.addWidget(self._sample_dist_le, row, 1)
-        layout.addWidget(QLabel("Rotation x (rad): "), row, 2, AR)
-        layout.addWidget(self._rx_le, row, 3)
-        layout.addWidget(QLabel("Rotation y (rad): "), row, 4, AR)
-        layout.addWidget(self._ry_le, row, 5)
-        layout.addWidget(QLabel("Rotation z (rad): "), row, 6, AR)
-        layout.addWidget(self._rz_le, row, 7)
+        param_layout.addWidget(QLabel("Sample distance (m): "), row, 0, AR)
+        param_layout.addWidget(self._sample_dist_le, row, 1)
+        param_layout.addWidget(QLabel("Rotation x (rad): "), row, 2, AR)
+        param_layout.addWidget(self._rx_le, row, 3)
+        param_layout.addWidget(QLabel("Rotation y (rad): "), row, 4, AR)
+        param_layout.addWidget(self._ry_le, row, 5)
+        param_layout.addWidget(QLabel("Rotation z (rad): "), row, 6, AR)
+        param_layout.addWidget(self._rz_le, row, 7)
 
         row += 1
-        layout.addWidget(QLabel("Photon energy (keV): "), row, 0, AR)
-        layout.addWidget(self._photon_energy_le, row, 1)
-        layout.addWidget(QLabel("Integ method: "), row, 2, AR)
-        layout.addWidget(self._integ_method_cb, row, 3)
-        layout.addWidget(QLabel("Integ points: "), row, 4, AR)
-        layout.addWidget(self._integ_pts_le, row, 5)
-        layout.addWidget(QLabel("Integ range (1/A): "), row, 6, AR)
-        layout.addWidget(self._integ_range_le, row, 7)
+        param_layout.addWidget(QLabel("Photon energy (keV): "), row, 0, AR)
+        param_layout.addWidget(self._photon_energy_le, row, 1)
+        param_layout.addWidget(QLabel("Integ method: "), row, 2, AR)
+        param_layout.addWidget(self._integ_method_cb, row, 3)
+        param_layout.addWidget(QLabel("Integ points: "), row, 4, AR)
+        param_layout.addWidget(self._integ_pts_le, row, 5)
+        param_layout.addWidget(QLabel("Integ range (1/A): "), row, 6, AR)
+        param_layout.addWidget(self._integ_range_le, row, 7)
 
         row += 1
-        layout.addWidget(QLabel("Norm: "), row, 0, AR)
-        layout.addWidget(self._norm_cb, row, 1)
-        layout.addWidget(QLabel("AUC range (1/A): "), row, 2, AR)
-        layout.addWidget(self._auc_range_le, row, 3)
-        layout.addWidget(QLabel("FOM range (1/A): "), row, 4, AR)
-        layout.addWidget(self._fom_integ_range_le, row, 5)
-
+        param_layout.addWidget(QLabel("Norm: "), row, 0, AR)
+        param_layout.addWidget(self._norm_cb, row, 1)
+        param_layout.addWidget(QLabel("AUC range (1/A): "), row, 2, AR)
+        param_layout.addWidget(self._auc_range_le, row, 3)
+        param_layout.addWidget(QLabel("FOM range (1/A): "), row, 4, AR)
+        param_layout.addWidget(self._fom_integ_range_le, row, 5)
+
+        param_widget.setLayout(param_layout)
+
+        algo_widget = QFrame()
+        algo_layout = QGridLayout()
+        algo_layout.addWidget(self._peak_finding_cb, 0, 0, 1, 2)
+        algo_layout.addWidget(QLabel("Peak prominence: "), 1, 0, AR)
+        algo_layout.addWidget(self._peak_prominence_le, 1, 1)
+        algo_layout.addWidget(QLabel("Peak slicer: "), 2, 0, AR)
+        algo_layout.addWidget(self._peak_slicer_le, 2, 1)
+        algo_widget.setLayout(algo_layout)
+
+        layout.addWidget(param_widget)
+        layout.addWidget(algo_widget)
+        layout.setContentsMargins(1, 1, 1, 1)
         self.setLayout(layout)
 
+        self.setFrameStyle(QFrame.NoFrame)
+        param_widget.setFrameStyle(QFrame.StyledPanel)
+        algo_widget.setFrameStyle(QFrame.StyledPanel)
+
     def initConnections(self):
         """Override."""
         mediator = self._mediator
@@ -178,6 +212,15 @@ def initConnections(self):
         self._fom_integ_range_le.value_changed_sgn.connect(
             mediator.onAiFomIntegRangeChange)
 
+        self._peak_finding_cb.toggled.connect(
+            mediator.onAiPeakFindingChange)
+
+        self._peak_prominence_le.value_changed_sgn.connect(
+            mediator.onAiPeakProminenceChange)
+
+        self._peak_slicer_le.value_changed_sgn.connect(
+            mediator.onAiPeakSlicerChange)
+
     def updateMetaData(self):
         """Override."""
         self._photon_energy_le.returnPressed.emit()
@@ -203,6 +246,10 @@ def updateMetaData(self):
 
         self._fom_integ_range_le.returnPressed.emit()
 
+        self._peak_finding_cb.toggled.emit(self._peak_finding_cb.isChecked())
+        self._peak_prominence_le.returnPressed.emit()
+        self._peak_slicer_le.returnPressed.emit()
+
         return True
 
     def loadMetaData(self):
@@ -223,3 +270,8 @@ def loadMetaData(self):
             self._available_norms_inv[int(cfg['normalizer'])])
         self._auc_range_le.setText(cfg['auc_range'][1:-1])
         self._fom_integ_range_le.setText(cfg['fom_integ_range'][1:-1])
+
+        self._updateWidgetValue(self._peak_finding_cb, cfg, "peak_finding")
+        self._updateWidgetValue(
+            self._peak_prominence_le, cfg, "peak_prominence")
+        self._updateWidgetValue(self._peak_slicer_le, cfg, "peak_slicer")

extra_foam/gui/ctrl_widgets/base_ctrl_widgets.py

@@ -10,10 +10,15 @@
 import abc
 
 from PyQt5.QtCore import Qt
-from PyQt5.QtWidgets import QFrame, QGroupBox
+from PyQt5.QtWidgets import (
+    QCheckBox, QComboBox, QFrame, QGroupBox, QLineEdit, QAbstractSpinBox
+)
 
+from .smart_widgets import SmartBoundaryLineEdit, SmartSliceLineEdit
+from ..gui_helpers import parse_slice_inv
 from ..mediator import Mediator
 from ...database import MetaProxy
+from ...logger import logger
 
 
 class _AbstractCtrlWidgetMixin:
@@ -50,6 +55,42 @@ def onStart(self):
     def onStop(self):
         raise NotImplementedError
 
+    def _updateWidgetValue(self, widget, config, key, *, cast=None):
+        """Update widget value from meta data."""
+        value = self._getMetaData(config, key)
+        if value is None:
+            return
+
+        if cast is not None:
+            value = cast(value)
+
+        if isinstance(widget, QCheckBox):
+            widget.setChecked(value == 'True')
+        elif isinstance(widget, SmartBoundaryLineEdit):
+            widget.setText(value[1:-1])
+        elif isinstance(widget, SmartSliceLineEdit):
+            widget.setText(parse_slice_inv(value))
+        elif isinstance(widget, QLineEdit):
+            widget.setText(value)
+        elif isinstance(widget, QAbstractSpinBox):
+            widget.setValue(value)
+        else:
+            logger.error(f"Unknown widget type: {type(widget)}")
+
+    @staticmethod
+    def _getMetaData(config, key):
+        """Convienient function to get metadata and capture key error.
+
+        :param dict config: config dictionary.
+        :param str key: meta data key.
+        """
+        try:
+            return config[key]
+        except KeyError:
+            # This happens when loading metadata in a new version with
+            # a config file in the old version.
+            logger.warning(f"Meta data key not found: {key}")
+
 
 class _AbstractCtrlWidget(QFrame, _AbstractCtrlWidgetMixin):
 

extra_foam/gui/ctrl_widgets/calibration_ctrl_widget.py

@@ -14,7 +14,7 @@
 
 from .base_ctrl_widgets import _AbstractCtrlWidget
 from .smart_widgets import SmartSliceLineEdit
-from ..gui_helpers import create_icon_button, parse_slice_inv
+from ..gui_helpers import create_icon_button
 from ...database import Metadata as mt
 
 
@@ -134,7 +134,5 @@ def loadMetaData(self):
         self._dark_as_offset_cb.setChecked(cfg["dark_as_offset"] == 'True')
 
         if self._pulse_resolved:
-            self._gain_cells_le.setText(
-                parse_slice_inv(cfg["gain_cells"]))
-            self._offset_cells_le.setText(
-                parse_slice_inv(cfg["offset_cells"]))
+            self._updateWidgetValue(self._gain_cells_le, cfg, "gain_cells")
+            self._updateWidgetValue(self._offset_cells_le, cfg, "offset_cells")

extra_foam/gui/ctrl_widgets/geometry_ctrl_widget.py

@@ -19,12 +19,13 @@
 )
 
 from .base_ctrl_widgets import _AbstractCtrlWidget
-from .smart_widgets import SmartLineEdit, SmartStringLineEdit
+from .smart_widgets import SmartLineEdit
 from ..gui_helpers import invert_dict
+from ..items import GeometryItem
 from ...config import config, GeomAssembler
 from ...database import Metadata as mt
 from ...geometries import module_indices
-from ..items import GeometryItem
+from ...logger import logger
 
 
 def _parse_table_widget(widget):
@@ -213,16 +214,21 @@ def loadMetaData(self):
 
         cfg = self._meta.hget_all(mt.GEOMETRY_PROC)
 
-        self._assembler_cb.setCurrentText(
-            self._assemblers_inv[int(cfg["assembler"])])
-        self._stack_only_cb.setChecked(cfg["stack_only"] == 'True')
-        self._geom_file_le.setText(cfg["geometry_file"])
+        assembler = self._getMetaData(cfg, "assembler")
+        if assembler is not None:
+            self._assembler_cb.setCurrentText(
+                self._assemblers_inv[int(cfg["assembler"])])
+
+        self._updateWidgetValue(self._stack_only_cb, cfg, "stack_only")
+        self._updateWidgetValue(self._geom_file_le, cfg, "geometry_file")
 
         # TODO: check number of modules for JungFrau
-        coordinates = json.loads(cfg["coordinates"], encoding='utf8')
-        table = self._coordinates_tb
-        n_rows = table.rowCount()
-        n_cols = table.columnCount()
-        for j in range(n_cols):
-            for i in range(n_rows):
-                table.cellWidget(i, j).setText(str(coordinates[j][i]))
+        coordinates = self._getMetaData(cfg, "coordinates")
+        if coordinates is not None:
+            coordinates = json.loads(coordinates, encoding='utf8')
+            table = self._coordinates_tb
+            n_rows = table.rowCount()
+            n_cols = table.columnCount()
+            for j in range(n_cols):
+                for i in range(n_rows):
+                    table.cellWidget(i, j).setText(str(coordinates[j][i]))

extra_foam/gui/ctrl_widgets/image_transform_ctrl_widget.py

@@ -162,17 +162,18 @@ def loadMetaData(self):
         """Override."""
         cfg = self._meta.hget_all(mt.IMAGE_TRANSFORM_PROC)
 
-        self._ma_window_le.setText(str(cfg["ma_window"]))
+        self._updateWidgetValue(self._ma_window_le, cfg, "ma_window")
 
         # do not load transform type since it is not an "input"
 
         fft = self._fourier_transform
-        fft.logrithmic_cb.setChecked(cfg["fft:logrithmic"] == 'True')
+        self._updateWidgetValue(fft.logrithmic_cb, cfg, "fft:logrithmic")
 
         ed = self._edge_detection
-        ed.kernel_size_sp.setValue(int(cfg["ed:kernel_size"]))
-        ed.sigma_sp.setValue(float(cfg["ed:sigma"]))
-        ed.threshold_le.setText(cfg['ed:threshold'][1:-1])
+        self._updateWidgetValue(
+            ed.kernel_size_sp, cfg, "ed:kernel_size", cast=int)
+        self._updateWidgetValue(ed.sigma_sp, cfg, "ed:sigma", cast=float)
+        self._updateWidgetValue(ed.threshold_le, cfg, "ed:threshold")
 
     def registerTransformType(self):
         self._mediator.onItTransformTypeChange(

extra_foam/gui/ctrl_widgets/pump_probe_ctrl_widget.py

@@ -17,7 +17,7 @@
 
 from .base_ctrl_widgets import _AbstractGroupBoxCtrlWidget
 from .smart_widgets import SmartSliceLineEdit
-from ..gui_helpers import invert_dict, parse_slice_inv
+from ..gui_helpers import invert_dict
 from ...config import PumpProbeMode, AnalysisType
 from ...database import Metadata as mt
 
@@ -140,10 +140,10 @@ def loadMetaData(self):
         self._abs_difference_cb.setChecked(cfg["abs_difference"] == 'True')
 
         if self._pulse_resolved:
-            self._on_pulse_le.setText(
-                parse_slice_inv(cfg["on_pulse_slicer"]))
-            self._off_pulse_le.setText(
-                parse_slice_inv(cfg["off_pulse_slicer"]))
+            self._updateWidgetValue(
+                self._on_pulse_le, cfg, "on_pulse_slicer")
+            self._updateWidgetValue(
+                self._off_pulse_le, cfg, "off_pulse_slicer")
 
     def onPpModeChange(self, pp_mode):
         if not self._pulse_resolved: