Dectris Arina version

DuSC_explorer/rotatable.py → DuSC_explorer/DuSC_dectris.py

@@ -1,10 +1,9 @@
 """
-Load TitanX data and show real and reciprocal space.
+Load Dectris Arina data and show real and reciprocal space.
 
-The real space ROI can be rotated
+Based on DuSC_explorer, but uses dense operations.
 
 author: Peter Ercius
-date: 2023/11/02
 
 """
 
@@ -13,15 +12,16 @@
 import pyqtgraph as pg
 from pyqtgraph.graphicsItems.ROI import Handle
 import numpy as np
-from scipy import ndimage
 import ncempy 
 from tifffile import imwrite
+import h5py
+import hdf5plugin
 
 from qtpy.QtWidgets import *
 from qtpy.QtCore import QRectF
 from qtpy import QtGui
 
-class fourD(QWidget):
+class DuSC(QWidget):
 
     def __init__(self, *args, **kwargs):
 
@@ -39,18 +39,13 @@ def __init__(self, *args, **kwargs):
         self.log_diffraction = True
         self.handle_size = 10
 
-        self.available_colormaps = ['thermal', 'flame', 'yellowy', 'bipolar', 'spectrum', 'cyclic', 'greyclip', 'grey',
-                                    'viridis', 'inferno', 'plasma', 'magma']
-        self.colormap = pg.colormap.getFromMatplotlib('grey')
+        self.available_colormaps = ['viridis', 'inferno', 'plasma', 'magma','cividis','CET-C5','CET-C5s']
+        self.colormap = 'cividis' # default colormap
 
-        super(fourD, self).__init__(*args, *kwargs)
-        self.setWindowTitle("NCEM: TitanX 4D Data Explorer")
+        super(DuSC, self).__init__(*args, *kwargs)
+        self.setWindowTitle("NCEM: Dectris Arina 4D Data Explorer")
         self.setWindowIcon(QtGui.QIcon('MF_logo_only_small.ico'))
 
-        # Set the update strategy to the JIT version
-        #self.update_real = self.update_real_stempy
-        #self.update_diffr = self.update_diffr_stempy
-
         # Add a graphics/view/image
         # Need to set invertY = True and row-major
         self.graphics = pg.GraphicsLayoutWidget()
@@ -129,8 +124,6 @@ def __init__(self, *args, **kwargs):
 
         self.open_file()
 
-        self.real_space_roi.addRotateHandle((0, 0), (0.5, 0.5))
-
         self.real_space_roi.sigRegionChanged.connect(self.update_diffr)
         self.diffraction_space_roi.sigRegionChanged.connect(self.update_real)
         self.real_space_roi.sigRegionChanged.connect(self._update_position_message)
@@ -149,7 +142,7 @@ def open_file(self):
         """
 
         fd = pg.FileDialog()
-        fd.setNameFilter("Sparse Stempy (*.dm3 *.dm4)")
+        fd.setNameFilter("Dectris (*_master.h5)")
         fd.setDirectory(str(self.current_dir))
         fd.setFileMode(pg.FileDialog.ExistingFile)
 
@@ -160,25 +153,22 @@ def open_file(self):
             self.setData(Path(file_names[0]))
 
     def setData(self, fPath):
-        """ Load the data from the DM file.
+        """ Load the data from the file.
 
         Parameters
         ----------
         fPath : pathlib.Path
             The path of to the file to load.
         """
         self.statusBar.showMessage("Loading the data...")
-
-        # Load data as a SparseArray class
-        with ncempy.io.dm.fileDM(fPath) as f0:
-            dm0 = f0.getDataset(0)
-
-            scanI = int(f0.allTags['.ImageList.2.ImageTags.Series.nimagesx'])
-            scanJ = int(f0.allTags['.ImageList.2.ImageTags.Series.nimagesy'])
-            numkI = dm0['data'].shape[2]
-            numkJ = dm0['data'].shape[1]
-
-            self.sa = dm0['data'].reshape([scanJ,scanI,numkJ,numkI])
+
+        # Load Dectris data
+        with ncempy.io.dectris.fileDECTRIS(fPath) as dectris:
+            self.sa = dectris.get_dataset(remove_bad_pixels=True)
+            scanI = self.sa.shape[0]
+            scanJ = self.sa.shape[1]
+            numkI = self.sa.shape[2]
+            numkJ = self.sa.shape[3]
 
         print('Data shape is {}'.format(self.sa.shape))
 
@@ -207,31 +197,22 @@ def setData(self, fPath):
 
         self.statusBar.showMessage('loaded {}'.format(fPath.name))
 
-
     def update_diffr(self):
         """ Update the diffraction space image by summing in real space
         """
-        # Get the region of the real space ROI
-        out = self.real_space_roi.getArrayRegion(self.dp, self.real_space_image_item,returnMappedCoords=True,order=0)
-        # Setup a mask with the correct dimensions
-        mask = np.zeros(self.scan_dimensions, dtype=bool)
-        mask[np.round(out[1][0].astype(np.uint16)), np.round(out[1][1]).astype(np.uint16)] = 1
-        ndimage.binary_closing(mask, output=mask)
 
-        out2 = self.real_space_roi.getArraySlice(self.dp, self.real_space_image_item)
-
-        temp = self.sa[out2[0][0],out2[0][1],:,:]
-        mask = mask[out2[0][0],out2[0][1]]
-        self.dp = temp.sum(axis=(0,1),where=mask[:,:,None,None], dtype=np.uint16)
-
+        self.dp = self.sa[int(self.real_space_roi.pos().y()) - 0:int(self.real_space_roi.pos().y() + self.real_space_roi.size().y()) + 1,
+                   int(self.real_space_roi.pos().x()) - 0:int(self.real_space_roi.pos().x() + self.real_space_roi.size().x()) + 1,
+                   :, :]
+        self.dp = self.dp.sum(axis=(0,1))
         self.diffraction_pattern_image_item.setImage(np.log(self.dp + 1))
 
     def update_real(self):
         """ Update the real space image by summing in diffraction space
         """
         self.rs = self.sa[:, :,
-                  int(self.diffraction_space_roi.pos().y()) - 1:int(self.diffraction_space_roi.pos().y() + self.diffraction_space_roi.size().y()) + 0,
-                  int(self.diffraction_space_roi.pos().x()) - 1:int(self.diffraction_space_roi.pos().x() + self.diffraction_space_roi.size().x()) + 0]
+                  int(self.diffraction_space_roi.pos().y()) - 0:int(self.diffraction_space_roi.pos().y() + self.diffraction_space_roi.size().y()) + 1,
+                  int(self.diffraction_space_roi.pos().x()) - 0:int(self.diffraction_space_roi.pos().x() + self.diffraction_space_roi.size().x()) + 1]
         self.rs = self.rs.sum(axis=(2, 3))
         self.real_space_image_item.setImage(self.rs, autoRange=True)
 
@@ -326,10 +307,18 @@ def _write_smv(self, out_path):
         with open(out_path, 'rb+') as f0:
             f0.seek(512, 0)
             f0.write(im)
-if __name__ == '__main__':
+
+def open_file():
+    """Start the graphical user interface by opening a file. This is used from a python interpreter."""
+    main()
+
+def main():
     """Main function used to start the GUI."""
 
     qapp = QApplication([])
-    fourD_view = fourD()
-    fourD_view.show()
+    DuSC_view = DuSC()
+    DuSC_view.show()
     qapp.exec_()
+
+if __name__ == '__main__':
+    main()