ayyerlab / clement Goto Github PK

It would be nice to have a waitbar or something that shows that the program is doing something and has not stoped/crashed.

The merged image cannot be recalculated with different channels. The basic problem is that the data_popup array is not correctly filled by the project loading process.

Points should appear in saved image
Points should have annotations, which will also be saved in .txt file

QGraphicsScene::removeItem: item 0x7fa732ea9c70's scene (0x0) is different from this scene (0x7fa72f608220)
QGraphicsScene::removeItem: item 0x7fa731c45570's scene (0x0) is different from this scene (0x7fa72f608220)
Traceback (most recent call last):
File "/Users/renerosch/miniconda3/envs/clement/lib/python3.7/site-packages/clement/em_controls.py", line 276, in _show_assembled
self._update_imview()
File "/Users/renerosch/miniconda3/envs/clement/lib/python3.7/site-packages/clement/em_controls.py", line 143, in _update_imview
self.imview.setImage(self.ops.data, levels=levels)
File "/Users/renerosch/miniconda3/envs/clement/lib/python3.7/site-packages/pyqtgraph/imageview/ImageView.py", line 273, in setImage
raise Exception("Can not interpret image with dimensions %s" % (str(img.shape)))
Exception: Can not interpret image with dimensions ()
Abort trap: 6
(clement) cssbhpi034-wlan:~ renerosch$

Assembling images into (954, 891)-shaped array...done
Defining grid on FM image: Click on corners
Done defining grid on FM image: Manually adjust fine positions
You have to select exactly 4 points. Try again!
Defining grid on FM image: Click on corners
Done defining grid on FM image: Manually adjust fine positions
Performing affine transformation on FM image
counter-clockwise
Input points:
[[ 433.84701318 904.47534444]
[ 936.84660532 1317.83144491]
[ 1350.20270579 834.7526287 ]
[ 852.18330764 386.53517036]]
ROI side length: 655.660948793 ± 13.4595223752
Transform matrix:
[[ 7.64036066e-01 6.34373517e-01 0.00000000e+00]
[ 6.57458206e-01 -7.63376609e-01 1.56339529e+03]
[ 0.00000000e+00 0.00000000e+00 1.00000000e+00]]
Traceback (most recent call last):
File "/Users/renerosch/miniconda3/lib/python3.6/site-packages/clement/base_controls.py", line 266, in _affine_transform
self.ops.calc_affine_transform(points)
File "/Users/renerosch/miniconda3/lib/python3.6/site-packages/clement/fm_operations.py", line 322, in calc_affine_transform
self.apply_transform()
File "/Users/renerosch/miniconda3/lib/python3.6/site-packages/clement/fm_operations.py", line 415, in apply_transform
self._tf_data[:,:,i] = ndi.affine_transform(self._orig_data[:,:,i], np.linalg.inv(self.tf_matrix), order=1, output_shape=self._tf_shape)
File "/Users/renerosch/miniconda3/lib/python3.6/site-packages/scipy/ndimage/interpolation.py", line 449, in affine_transform
raise RuntimeError('affine matrix has wrong number of rows')
RuntimeError: affine matrix has wrong number of rows
Abort trap: 6
(Clement) cssbhpi034-wlan:Downloads renerosch$ clement

QGraphicsScene::removeItem: item 0x7fa732ea9c70's scene (0x0) is different from this scene (0x7fa72f608220)
QGraphicsScene::removeItem: item 0x7fa731c45570's scene (0x0) is different from this scene (0x7fa72f608220)
Traceback (most recent call last):
File "/Users/renerosch/miniconda3/envs/clement/lib/python3.7/site-packages/clement/em_controls.py", line 276, in _show_assembled
self._update_imview()
File "/Users/renerosch/miniconda3/envs/clement/lib/python3.7/site-packages/clement/em_controls.py", line 143, in _update_imview
self.imview.setImage(self.ops.data, levels=levels)
File "/Users/renerosch/miniconda3/envs/clement/lib/python3.7/site-packages/pyqtgraph/imageview/ImageView.py", line 273, in setImage
raise Exception("Can not interpret image with dimensions %s" % (str(img.shape)))
Exception: Can not interpret image with dimensions ()
Abort trap: 6
(clement) cssbhpi034-wlan:~ renerosch$

Human readability and easy editability is preferable