Merge pull request #270 from zhujun98/implement_pulse_resolved_correl…

…ation

Implement pulse resolved correlation

docs/special_suite.rst

@@ -89,7 +89,7 @@ More info on command line arguments can be obtained as
 General purposed apps
 ---------------------
 
-Camera view, multi-camera view
+:ref:`Camera view`, :ref:`Vector view`, multi-camera view
 
 
 .. _Camera view:
@@ -122,6 +122,37 @@ More small features will be added in the future.
 +----------------------------+--------------------------------------------------------------------+
 
 
+.. _Vector view:
+
+Vector view
+"""""""""""
+
+.. image:: images/special_suite_vector_view.jpg
+   :width: 800
+
+Vector view helps you monitor 1D data like XGM intensity, digitizer pulse integral, pulse-resolved
+ROI FOM and the correlation between them. **Vector view receives processed data from a main EXtra-foam
+instance.**
+
++----------------------------+--------------------------------------------------------------------+
+| Input                      | Description                                                        |
++============================+====================================================================+
+| ``Vector1``                | Vector 1.                                                          |
++----------------------------+--------------------------------------------------------------------+
+| ``Vector2``                | Vector 2 (optional).                                               |
++----------------------------+--------------------------------------------------------------------+
+
+.. note::
+    In order to correlate two vectors, you will need to use the `Pulse slicer` in the data source
+    tree located in the main GUI to select the data.
+
+.. warning::
+    To have the pulse-resolved ROI FOM data, currently you must open the :ref:`Histogram` window
+    in the main GUI and select `ROI FOM` as the analysis type. This will activate the pulse-resolved
+    ROI FOM calculation, which is a little bit expensive. Also, make sure the `Pulse resolved`
+    checkbox is checked.
+
+
 Special purposed apps
 ---------------------
 

extra_foam/special_suite/facade.py

@@ -23,6 +23,7 @@
 from .module_scan_w import ModuleScanWindow
 from .multicam_view_w import MultiCamViewWindow
 from .trxas_w import TrXasWindow
+from .vector_view import VectorViewWindow
 from .xas_tim_w import XasTimWindow
 from .xas_tim_xmcd_w import XasTimXmcdWindow
 from .xes_timing_w import XesTimingWindow
@@ -82,8 +83,10 @@ def initUI(self):
             layout_row.setRowStretch(2, 2)
         self._cw.setLayout(layout)
 
-        self.setFixedSize(
-            self._WIDTH, (len(self._buttons) // 4 + 1) * self._ROW_HEIGHT)
+        h = len(self._buttons) // 4
+        if len(self._buttons) % 4 != 0:
+            h += 1
+        self.setFixedSize(self._WIDTH, h * self._ROW_HEIGHT)
 
     def addSpecial(self, instance_type):
         """Add a button for the given analysis."""
@@ -98,6 +101,7 @@ def addSpecial(self, instance_type):
 
     def addCommonSpecials(self):
         self.addSpecial(CamViewWindow)
+        self.addSpecial(VectorViewWindow)
         self.addSpecial(MultiCamViewWindow)
 
 
@@ -118,6 +122,8 @@ def __init__(self):
         super().__init__("FXE")
 
         self.addSpecial(XesTimingWindow)
+        self.addSpecial(GotthardWindow)
+        self.addSpecial(GotthardPumpProbeWindow)
         self.addCommonSpecials()
 
         self.initUI()
@@ -151,6 +157,18 @@ def __init__(self):
         self.show()
 
 
+class HedSpecialSuiteFacade(_SpecialSuiteFacadeBase):
+    def __init__(self):
+        super().__init__("HED")
+
+        self.addSpecial(GotthardWindow)
+        self.addSpecial(GotthardPumpProbeWindow)
+        self.addCommonSpecials()
+
+        self.initUI()
+        self.show()
+
+
 class DetSpecialSuiteFacade(_SpecialSuiteFacadeBase):
     def __init__(self):
         super().__init__("DET")
@@ -175,6 +193,9 @@ def create_special_suite(topic):
     if topic == "MID":
         return MidSpecialSuiteFacade()
 
+    if topic == "HED":
+        return HedSpecialSuiteFacade()
+
     if topic == "DET":
         return DetSpecialSuiteFacade()
 

extra_foam/special_suite/special_analysis_base.py

@@ -512,6 +512,37 @@ def squeezeToImage(self, tid, arr):
 
         return img
 
+    def squeezeToVector(self, tid, arr):
+        """Try to squeeze an array to get a 1D vector data.
+
+        It attempts to squeeze the input array if its dimension is 2D.
+
+        :param int tid: train ID.
+        :param numpy.ndarray arr: image data.
+        """
+        if arr is None:
+            return
+
+        if arr.ndim not in (1, 2):
+            self.log.error(f"[{tid}] Array dimension must be either 1 or 2! "
+                           f"actual {arr.ndim}!")
+            return
+
+        if arr.ndim == 2:
+            try:
+                img = np.squeeze(arr, axis=0)
+            except ValueError:
+                try:
+                    img = np.squeeze(arr, axis=-1)
+                except ValueError:
+                    self.log.error(
+                        "f[{tid}] Failed to squeeze a 2D array to 1D!")
+                    return
+        else:
+            img = arr
+
+        return img
+
     def getRoiData(self, img, copy=False):
         """Get the ROI(s) of an image or arrays of images.
 

extra_foam/special_suite/tests/test_special_analysis_base.py

@@ -292,6 +292,22 @@ def testRoiCtrl(self):
         pass
 
     def testSqueezeCameraImage(self):
+        a1d = np.ones((4, ))
+        a2d = np.ones((2, 1))
+        a3d = np.ones((3, 3, 1))
+
+        func = functools.partial(self._win._worker_st.squeezeToVector, 1234)
+
+        assert func(None) is None
+        assert func(a3d) is None
+
+        ret_1d = func(a1d)
+        np.testing.assert_array_equal(a1d, ret_1d)
+
+        ret_2d = func(a2d)
+        np.testing.assert_array_equal(a2d.squeeze(axis=-1), ret_2d)
+
+    def testSqueezeToVector(self):
         a1d = np.ones((4, ))
         a2d = np.ones((2, 2))
         a3d = np.ones((3, 3, 1))

extra_foam/special_suite/tests/test_vectorview.py

@@ -0,0 +1,108 @@
+from collections import Counter
+
+import pytest
+import numpy as np
+
+from extra_foam.pipeline.tests import _TestDataMixin
+
+from extra_foam.special_suite import logger, mkQApp
+from extra_foam.pipeline.exceptions import ProcessingError
+from extra_foam.special_suite.vector_view import (
+    VectorViewProcessor, VectorViewWindow, VectorPlot, VectorCorrelationPlot,
+    InTrainVectorCorrelationPlot
+)
+
+from . import _SpecialSuiteWindowTestBase, _SpecialSuiteProcessorTestBase
+
+
+app = mkQApp()
+
+logger.setLevel('INFO')
+
+
+class TestCamViewWindow(_SpecialSuiteWindowTestBase):
+    @classmethod
+    def setUpClass(cls):
+        cls._win = VectorViewWindow('SCS')
+
+    @classmethod
+    def tearDownClass(cls):
+        # explicitly close the MainGUI to avoid error in GuiLogger
+        cls._win.close()
+
+    @staticmethod
+    def data4visualization():
+        """Override."""
+        return {
+            "vector1": np.arange(10),
+            "vector2": np.arange(10) + 5,
+            "vector1_full": np.arange(100),
+            "vector2_full": np.arange(100) + 5,
+        }
+
+    def testWindow(self):
+        win = self._win
+
+        self.assertEqual(3, len(win._plot_widgets_st))
+        counter = Counter()
+        for key in win._plot_widgets_st:
+            counter[key.__class__] += 1
+
+        self.assertEqual(1, counter[VectorPlot])
+        self.assertEqual(1, counter[InTrainVectorCorrelationPlot])
+        self.assertEqual(1, counter[VectorCorrelationPlot])
+
+        self._check_update_plots()
+
+    def testCtrl(self):
+        win = self._win
+        ctrl_widget = win._ctrl_widget_st
+        proc = win._worker_st
+
+        # test default values
+        self.assertEqual('XGM intensity', proc._vector1)
+        self.assertEqual('', proc._vector2)
+
+        # test set new values
+        widget = ctrl_widget.vector1_cb
+        widget.setCurrentText("ROI FOM")
+        self.assertEqual("ROI FOM", proc._vector1)
+
+        widget = ctrl_widget.vector2_cb
+        widget.setCurrentText("Digitizer pulse integral")
+        self.assertEqual("Digitizer pulse integral", proc._vector2)
+
+
+class TestVectorViewProcessor(_TestDataMixin, _SpecialSuiteProcessorTestBase):
+    @pytest.fixture(autouse=True)
+    def setUp(self):
+        self._proc = VectorViewProcessor(object(), object())
+        self._proc._vector1 = "XGM intensity"
+
+    def testProcessing(self):
+        data, processed = self.simple_data(1001, (4, 2, 2))
+        proc = self._proc
+
+        with pytest.raises(ProcessingError, match="XGM intensity is not available"):
+            proc.process(data)
+
+        processed.pulse.xgm.intensity = np.random.rand(4)
+        ret = proc.process(data)
+        self._check_processed_data_structure(ret)
+
+        self._proc._vector2 = "ROI FOM"
+        processed.pulse.roi.fom = np.random.rand(5)
+        with pytest.raises(ProcessingError, match="Vectors have different lengths"):
+            proc.process(data)
+        processed.pulse.roi.fom = np.random.rand(4)
+        proc.process(data)
+
+        self._proc._vector2 = "Digitizer pulse integral"
+        processed.pulse.digitizer.ch_normalizer = 'B'
+        processed.pulse.digitizer['B'].pulse_integral = np.random.rand(4)
+        proc.process(data)
+
+    def _check_processed_data_structure(self, ret):
+        """Override."""
+        data_gt = TestCamViewWindow.data4visualization().keys()
+        assert set(ret.keys()) == set(data_gt)