Merge pull request #1761 from bnmajor/fiddle-instrument

Fiddle instrument

Author: psavery

hexrdgui/constants.py

@@ -78,6 +78,11 @@ class PolarXAxisType:
 
 DOCUMENTATION_URL = 'https://hexrdgui.readthedocs.io/'
 
+FIDDLE_HDF5_PATH = [
+    'ATTRIBUTES/SHOT_IMAGE/ATTRIBUTES/FRAME_IMAGESFRAME_IMAGES/0/DATA',
+    'DATA'
+]
+
 KNOWN_HDF5_PATHS = [
     ['ATTRIBUTES/TARGET_ORIENTED_IMAGE/DATA', 'DATA'],
     ['ATTRIBUTES/PINHOLE_ORIENTED_IMAGE/DATA', 'DATA'],
@@ -87,6 +92,7 @@ class PolarXAxisType:
     ['ATTRIBUTES/TIME_ADJUSTED_IMAGE/DATA', 'DATA'],
     ['ATTRIBUTES/PSL_IMAGE/DATA', 'DATA'],
     ['DATA', 'DATA'],
+    FIDDLE_HDF5_PATH,
 ]
 
 DEFAULT_LIMITED_CMAPS = [
@@ -99,6 +105,7 @@ class LLNLTransform:
     IP3 = UI_TRANS_INDEX_FLIP_VERTICALLY
     IP4 = UI_TRANS_INDEX_FLIP_VERTICALLY
     PXRDIP = UI_TRANS_INDEX_FLIP_HORIZONTALLY
+    FIDDLE = UI_TRANS_INDEX_FLIP_HORIZONTALLY
 
 
 KNOWN_DETECTOR_NAMES = {
@@ -145,3 +152,5 @@ class LLNLTransform:
     "Rotate 180°",
     "Rotate 270°"
 ]
+
+FIDDLE_FRAMES = 4

hexrdgui/hexrd_config.py

@@ -9,6 +9,7 @@
 import h5py
 import matplotlib
 import numpy as np
+from scipy.signal import medfilt2d
 import yaml
 
 import hexrd.imageseries.save
@@ -18,6 +19,7 @@
 from hexrd.instrument.physics_package import HEDPhysicsPackage
 from hexrd.material import load_materials_hdf5, save_materials_hdf5, Material
 from hexrd.rotations import RotMatEuler
+from hexrd.utils.decorators import memoize
 from hexrd.utils.yaml import NumpyToNativeDumper
 from hexrd.valunits import valWUnit
 
@@ -331,6 +333,7 @@ def __init__(self):
         self._physics_package = None
         self._detector_coatings = {}
         self._instrument_rigid_body_params = {}
+        self._median_filer_correction = {}
 
         # Make sure that the matplotlib font size matches the application
         self.font_size = self.font_size
@@ -434,6 +437,8 @@ def _attributes_to_persist(self):
             ('custom_polar_tth_distortion_object_serialized', None),
             ('detector_coatings_dictified', {}),
             ('overlays_dictified', []),
+            ('apply_median_filter_correction', False),
+            ('median_filter_kernel_size', 7),
         ]
 
     # Provide a mapping from attribute names to the keys used in our state
@@ -563,6 +568,8 @@ def load_from_state(self, state):
             self.show_all_colormaps = self.show_all_colormaps == 'true'
         if not isinstance(self.apply_absorption_correction, bool):
             self.apply_absorption_correction = self.apply_absorption_correction == 'true'
+        if not isinstance(self.apply_median_filter_correction, bool):
+            self.apply_median_filter_correction = self.apply_median_filter_correction == 'true'
 
         # This is None sometimes. Make sure it is an empty list instead.
         if self.recent_state_files is None:
@@ -973,6 +980,13 @@ def intensity_corrected_images_dict(self):
             for name, img in images_dict.items():
                 images_dict[name] = img - minimum
 
+        if HexrdConfig().apply_median_filter_correction:
+            for name, img in images_dict.items():
+                images_dict[name] = medfilt2d_memoized(
+                    img,
+                    kernel_size=HexrdConfig().median_filter_kernel_size
+                )
+
         return images_dict
 
     @property
@@ -2479,6 +2493,7 @@ def any_intensity_corrections(self):
             'apply_lorentz_correction',
             'intensity_subtract_minimum',
             'apply_absorption_correction',
+            'apply_median_filter_correction',
         ]
 
         return any(getattr(self, x) for x in corrections)
@@ -2992,3 +3007,30 @@ def update_detector_phosphor(self, det_name, **kwargs):
         self._set_detector_coatings('phosphor')
         phosphor = self._detector_coatings[det_name]['phosphor']
         phosphor.deserialize(**kwargs)
+
+    @property
+    def apply_median_filter_correction(self):
+        return self._median_filer_correction.get('apply', False)
+
+    @apply_median_filter_correction.setter
+    def apply_median_filter_correction(self, v):
+        if v != self.apply_median_filter_correction:
+            self._median_filer_correction['apply'] = v
+            self.deep_rerender_needed.emit()
+
+    @property
+    def median_filter_kernel_size(self):
+        return self._median_filer_correction.get('kernel', 7)
+
+    @median_filter_kernel_size.setter
+    def median_filter_kernel_size(self, v):
+        if v != self.median_filter_kernel_size:
+            self._median_filer_correction['kernel'] = int(v)
+            self.deep_rerender_needed.emit()
+
+
+# This is set to (num_fiddle_plates * num_time_steps) + num_image_plates
+# This feature is primarily for FIDDLE
+@memoize(maxsize=21)
+def medfilt2d_memoized(img: np.ndarray, kernel_size: int):
+    return medfilt2d(img, kernel_size)

hexrdgui/interactive_template.py

@@ -69,7 +69,7 @@ def key_rotation_angle(self):
     @key_rotation_angle.setter
     def key_rotation_angle(self, angle=None):
         if angle is None:
-            angle = KEY_ROTATE_ANGLE
+            angle = KEY_ROTATE_ANGLE_FINE
         self._key_angle = angle
 
     def update_image(self, img):
@@ -83,10 +83,15 @@ def rotate_shape(self, angle):
     def create_polygon(self, verts, **polygon_kwargs):
         self.complete = False
         self.shape = patches.Polygon(verts, **polygon_kwargs)
+        self.outer_polygon = self.shape
         if has_nan(verts):
             # This template contains more than one polygon and the last point
             # should not be connected to the first. See Tardis IP for example.
             self.shape.set_closed(False)
+            # For the sake of checking events we only need the outer polygon
+            nans = np.where(np.isnan(verts))
+            boundary = self.shape.xy[:nans[0][0]]
+            self.outer_polygon = patches.Polygon(boundary)
         self.shape_styles.append(polygon_kwargs)
         self.update_position()
         self.connect_translate_rotate()
@@ -331,7 +336,7 @@ def on_press_translate(self, event):
         if event.inaxes != self.shape.axes or self.event_key == 'shift':
             return
 
-        contains, info = self.shape.contains(event)
+        contains, info = self.outer_polygon.contains(event)
         if not contains:
             return
         self.press = self.shape.xy, event.xdata, event.ydata
@@ -366,7 +371,7 @@ def on_press_rotate(self, event):
         if event.inaxes != self.shape.axes or self.event_key != 'shift':
             return
 
-        contains, info = self.shape.contains(event)
+        contains, info = self.outer_polygon.contains(event)
         if not contains:
             return
         # FIXME: Need to come back to this to understand why we