WIP: Generic binding for nanvar and nanstd

docs/image_tool.rst

@@ -9,13 +9,12 @@ IMAGE TOOL
 The *ImageTool* window is the second control window which provides various image-related
 information and controls.
 
+.. image:: images/ImageTool.png
+   :width: 800
 
 Image control
 -------------
 
-.. image:: images/ImageTool.png
-   :width: 800
-
 +----------------------------+--------------------------------------------------------------------+
 | Input                      | Description                                                        |
 +============================+====================================================================+
@@ -40,24 +39,45 @@ Image control
 +----------------------------+--------------------------------------------------------------------+
 
 
-Mask image
+Mask panel
 """"""""""
 
-The action bar provides several actions for real-time masking operation. The pixel values in the
-masked region will be set to 0.
+.. image:: images/mask_panel.png
+
+Besides the nan pixels inherited from the calibration pipeline, users are allowed to mask additional
+pixels to nan in this panel with threshold mask, tile edge mask and image mask.
+
+It should be noted that image mask is treated differently in **EXtra-foam**. One can draw and erase
+image mask at run time as well as save/load it as an assembled image or in modules if the detector
+has a geometry. Nan pixels outside the masked region of the image mask will not be saved and thus
+will also not be overwritten after loading an image mask from file.
 
 +----------------------------+--------------------------------------------------------------------+
 | Input                      | Description                                                        |
 +============================+====================================================================+
-| ``Mask``                   | Mask a rectangular region.                                         |
+| ``Threshold mask``         | An interval that pixels with values outside the interval will be   |
+|                            | masked. Please distinguish *threshold mask* from clipping_.        |
 +----------------------------+--------------------------------------------------------------------+
-| ``Unmask``                 | Remove mask in a rectangular region.                               |
+| ``Mask tile edges``        | Mask the edge pixel of each tile. *Only applicable for AGIPD, LPD  |
+|                            | and DSSC if EXtra-foam is selected as the* ``Assembler`` *in*      |
+|                            | :ref:`Geometry`.                                                   |
++----------------------------+--------------------------------------------------------------------+
+| ``Draw``                   | Draw mask in a rectangular region.                                 |
++----------------------------+--------------------------------------------------------------------+
+| ``Erase``                  | Erase mask in a rectangular region.                                |
 +----------------------------+--------------------------------------------------------------------+
-| ``Trash mask``             | Remove all the mask.                                               |
+| ``Remove mask``            | Remove the image mask.                                             |
 +----------------------------+--------------------------------------------------------------------+
-| ``Save image mask``        | Save the current image mask in `.npy` format.                      |
+| ``Load mask``              | Load an image mask in `.npy` format. The dtype of the loaded       |
+|                            | numpy array will be casted into bool if it is not. For detectors   |
+|                            | with a geometry, it is allowed to load an image mask in modules,   |
+|                            | i.e., an array which has the shape (modules, ss, fs).              |
 +----------------------------+--------------------------------------------------------------------+
-| ``Load image mask``        | Load a image mask in `.npy` format.                                |
+| ``Save mask``              | Save the current image mask in `.npy` format.                      |
++----------------------------+--------------------------------------------------------------------+
+| ``Save mask in modules``   | Save image mask in modules. *Only applicable for AGIPD, LPD        |
+|                            | and DSSC if EXtra-foam is selected as the* ``Assembler`` *in*      |
+|                            | :ref:`Geometry`.                                                   |
 +----------------------------+--------------------------------------------------------------------+
 
 

extra_foam/config.py

@@ -294,6 +294,8 @@ class _Config(dict):
         "GUI_CORRELATION_COLORS": (('b', 'r'), ('g', 'p')),
         # color of the image mask bounding box while drawing
         "GUI_MASK_BOUNDING_BOX_COLOR": 'b',
+        # color of the masked area for MaskItem
+        "GUI_MASK_FILL_COLOR": 'g',
         # -------------------------------------------------------------
         # Misc
         # -------------------------------------------------------------

extra_foam/geometries/__init__.py

@@ -27,13 +27,24 @@
 
 class _1MGeometryPyMixin:
     def output_array_for_position_fast(self, extra_shape=(), dtype=_IMAGE_DTYPE):
-        """Match the EXtra-geom signature."""
+        """Make an array with the shape of assembled data filled with nan.
+
+        Match the EXtra-geom signature.
+        """
         shape = extra_shape + tuple(self.assembledShape())
+        if dtype == np.bool:
+            return np.full(shape, 0, dtype=dtype)
         return np.full(shape, np.nan, dtype=dtype)
 
     def position_all_modules(self, modules, out, *, ignore_tile_edge=False):
-        """Match the EXtra-geom signature.
+        """Assemble data in modules according to where the pixels are.
 
+        Match the EXtra-geom signature.
+
+        :param numpy.ndarray/list modules: data in modules.
+            Shape = (memory cells, modules, y x) / (modules, y, x)
+        :param numpy.ndarray out: assembled data.
+            Shape = (memory cells, y, x) / (y, x)
         :param ignore_tile_edge: True for ignoring the pixels at the edges
             of tiles. If 'out' is pre-filled with nan, it it equivalent to
             masking the tile edges. This is an extra feature which does not
@@ -47,6 +58,23 @@ def position_all_modules(self, modules, out, *, ignore_tile_edge=False):
                 ml.append(modules[:, i, ...])
             self.positionAllModules(ml, out, ignore_tile_edge)
 
+    def output_array_for_dismantle_fast(self, extra_shape=(), dtype=_IMAGE_DTYPE):
+        """Make an array with the shape of data in modules filled with nan."""
+        shape = extra_shape + (self.n_modules, *self.module_shape)
+        if dtype == np.bool:
+            return np.full(shape, 0, dtype=dtype)
+        return np.full(shape, np.nan, dtype=dtype)
+
+    def dismantle_all_modules(self, assembled, out):
+        """Dismantle assembled data into data in modules.
+
+        :param numpy.ndarray out: assembled data.
+            Shape = (memory cells, y, x) / (y, x)
+        :param numpy.ndarray out: data in modules.
+            Shape = (memory cells, modules, y x) / (modules, y, x)
+        """
+        self.dismantleAllModules(assembled, out)
+
 
 class DSSC_1MGeometryFast(_DSSC_1MGeometry, _1MGeometryPyMixin):
     """DSSC_1MGeometryFast.

extra_foam/geometries/tests/test_1M_geometry.py

@@ -20,7 +20,7 @@
 
 
 class _Test1MGeometryMixin:
-    @pytest.mark.parametrize("dtype", [_IMAGE_DTYPE, _RAW_IMAGE_DTYPE])
+    @pytest.mark.parametrize("dtype", [_IMAGE_DTYPE, _RAW_IMAGE_DTYPE, bool])
     def testAssemblingSinglePulse(self, dtype):
         modules = np.ones((self.n_modules, *self.module_shape), dtype=dtype)
 
@@ -38,7 +38,13 @@ def testAssemblingSinglePulse(self, dtype):
         assert out_gt.shape == out_fast.shape
         np.testing.assert_array_equal(out_fast, out_gt)
 
-    @pytest.mark.parametrize("dtype", [_IMAGE_DTYPE, _RAW_IMAGE_DTYPE])
+        # test dismantle
+        dismantled_out = self.geom_fast.output_array_for_dismantle_fast(dtype=_IMAGE_DTYPE)
+        self.geom_fast.dismantle_all_modules(out_fast, dismantled_out)
+
+        np.testing.assert_array_equal(modules, dismantled_out)
+
+    @pytest.mark.parametrize("dtype", [_IMAGE_DTYPE, _RAW_IMAGE_DTYPE, bool])
     def testAssemblingBridge(self, dtype):
         modules = np.ones((self.n_pulses, self.n_modules, *self.module_shape), dtype=dtype)
 
@@ -56,7 +62,13 @@ def testAssemblingBridge(self, dtype):
         assert out_gt.shape == out_fast.shape
         np.testing.assert_array_equal(out_fast, out_gt)
 
-    @pytest.mark.parametrize("dtype", [_IMAGE_DTYPE, _RAW_IMAGE_DTYPE])
+        # test dismantle
+        dismantled_out = self.geom_fast.output_array_for_dismantle_fast((self.n_pulses,), dtype=_IMAGE_DTYPE)
+        self.geom_fast.dismantle_all_modules(out_fast, dismantled_out)
+
+        np.testing.assert_array_equal(modules, dismantled_out)
+
+    @pytest.mark.parametrize("dtype", [_IMAGE_DTYPE, _RAW_IMAGE_DTYPE, bool])
     def testAssemblingFile(self, dtype):
         modules = StackView(
             {i: np.ones((self.n_pulses, *self.module_shape), dtype=dtype) for i in range(self.n_modules)},

extra_foam/gui/ctrl_widgets/mask_ctrl_widget.py

@@ -47,9 +47,15 @@ def __init__(self, *args, **kwargs):
         self._non_reconfigurable_widgets = [
             self.save_btn,
             self.load_btn,
-            self.mask_save_in_modules_cb
         ]
 
+        if not self._require_geometry:
+            self.mask_tile_cb.setDisabled(True)
+            self.mask_save_in_modules_cb.setDisabled(True)
+        else:
+            self._non_reconfigurable_widgets.append(
+                self.mask_save_in_modules_cb)
+
         self.initUI()
         self.initConnections()
 
@@ -62,9 +68,8 @@ def initUI(self):
         layout.addWidget(QLabel("Threshold mask: "), row, 0, AR)
         layout.addWidget(self.threshold_mask_le, row, 1)
 
-        if self._require_geometry:
-            row += 1
-            layout.addWidget(self.mask_tile_cb, row, 0, AR)
+        row += 1
+        layout.addWidget(self.mask_tile_cb, row, 0, AR)
 
         row += 1
         sub_layout = QHBoxLayout()
@@ -108,8 +113,12 @@ def _onAssemblerChange(self, assembler):
         if assembler == GeomAssembler.EXTRA_GEOM:
             self.mask_tile_cb.setChecked(False)
             self.mask_tile_cb.setEnabled(False)
+
+            self.mask_save_in_modules_cb.setChecked(False)
+            self.mask_save_in_modules_cb.setEnabled(False)
         else:
             self.mask_tile_cb.setEnabled(True)
+            self.mask_save_in_modules_cb.setEnabled(True)
 
     def updateMetaData(self):
         """Override."""
@@ -125,8 +134,8 @@ def loadMetaData(self):
         self.threshold_mask_le.setText(cfg["threshold_mask"][1:-1])
         if self._require_geometry:
             self.mask_tile_cb.setChecked(cfg["mask_tile"] == 'True')
-        self.mask_save_in_modules_cb.setChecked(
-            cfg["mask_save_in_modules"] == 'True')
+            self.mask_save_in_modules_cb.setChecked(
+                cfg["mask_save_in_modules"] == 'True')
 
     @pyqtSlot(bool)
     def _updateExclusiveBtns(self, checked):

extra_foam/gui/image_tool/corrected_view.py

@@ -14,7 +14,6 @@
     QHBoxLayout, QSplitter, QVBoxLayout, QWidget
 )
 
-from .simple_image_data import _SimpleImageData
 from .base_view import _AbstractImageToolView, create_imagetool_view
 from ..plot_widgets import HistMixin, ImageAnalysis, PlotWidgetF
 from ..ctrl_widgets import (
@@ -140,7 +139,7 @@ def initConnections(self):
     def updateF(self, data, auto_update):
         """Override."""
         if auto_update or self._corrected.image is None:
-            self._corrected.setImageData(_SimpleImageData(data.image))
+            self._corrected.setImage(data.image)
             self._roi_proj_plot.updateF(data)
             self._roi_hist.updateF(data)
 

extra_foam/gui/image_tool/tests/test_image_tool.py

@@ -1,5 +1,5 @@
 import unittest
-from unittest.mock import MagicMock, patch
+from unittest.mock import MagicMock, patch, PropertyMock
 import math
 import os
 import tempfile
@@ -76,7 +76,6 @@ def setUp(self):
         self.image_tool = self.gui._image_tool
 
         self.view = self.image_tool._corrected_view.imageView
-        self.view.setImageData(None)
         self.view._image = None
 
         self.pulse_worker._image_proc = ImageProcessor()
@@ -247,9 +246,11 @@ def testMaskCtrlWidget(self):
         self.assertEqual(False, widget.mask_tile_cb.isChecked())
         self.assertEqual(False, widget.mask_save_in_modules_cb.isChecked())
 
+    @patch("extra_foam.pipeline.processors.ImageProcessor._require_geom",
+           new_callable=PropertyMock, create=True, return_value=False)
     @patch("extra_foam.pipeline.processors.image_assembler.ImageAssemblerFactory.BaseAssembler.process",
            side_effect=lambda x: x)
-    def testDrawMask(self, patched_process):
+    def testDrawMask(self, patched_process, require_geometry):
         # TODO: test by really drawing something on ImageTool
         from extra_foam.ipc import ImageMaskPub
 
@@ -777,6 +778,7 @@ def testGeometryCtrlWidget(self):
         # prepare for the following test
         widget._stack_only_cb.setChecked(True)
         mask_ctrl_widget.mask_tile_cb.setChecked(True)
+        mask_ctrl_widget.mask_save_in_modules_cb.setChecked(True)
         image_proc.update()
         self.assertTrue(assembler._stack_only)
         self.assertTrue(assembler._mask_tile)
@@ -788,6 +790,8 @@ def testGeometryCtrlWidget(self):
         self.assertFalse(widget._stack_only_cb.isChecked())
         self.assertFalse(mask_ctrl_widget.mask_tile_cb.isEnabled())
         self.assertFalse(mask_ctrl_widget.mask_tile_cb.isChecked())
+        self.assertFalse(mask_ctrl_widget.mask_save_in_modules_cb.isEnabled())
+        self.assertFalse(mask_ctrl_widget.mask_save_in_modules_cb.isChecked())
         widget._geom_file_le.setText("/geometry/file/")
         for i in range(4):
             for j in range(2):
@@ -803,6 +807,7 @@ def testGeometryCtrlWidget(self):
         widget._assembler_cb.setCurrentText(assemblers_inv[GeomAssembler.OWN])
         self.assertTrue(widget._stack_only_cb.isEnabled())
         self.assertTrue(mask_ctrl_widget.mask_tile_cb.isEnabled())
+        self.assertTrue(mask_ctrl_widget.mask_save_in_modules_cb.isEnabled())
 
         # test loading meta data
         mediator = widget._mediator
@@ -895,14 +900,18 @@ def testGeometryCtrlWidget(self):
 
     def testMaskCtrlWidget(self):
         widget = self.image_tool._mask_ctrl_widget
-        self.assertEqual(-1, widget.layout().indexOf(widget.mask_tile_cb))
+
+        self.assertFalse(widget.mask_tile_cb.isEnabled())
+        self.assertFalse(widget.mask_save_in_modules_cb.isEnabled())
 
         # test loading meta data
         # test if the meta data is invalid
         mediator = widget._mediator
         mediator.onImageMaskTileEdgeChange(True)
+        mediator.onImageMaskSaveInModulesToggled(True)
         widget.loadMetaData()
-        self.assertEqual(False, widget.mask_tile_cb.isChecked())
+        self.assertFalse(widget.mask_tile_cb.isChecked())
+        self.assertFalse(widget.mask_save_in_modules_cb.isChecked())
 
     def testCalibrationCtrlWidget(self):
         widget = self.image_tool._calibration_view._ctrl_widget