error reading DICOM CT: TypeError: Cannot cast ufunc multiply output

[Elaine Meng]

for example, the CT subdirectory in the same dataset as attached to ticket #1662

UCSF ChimeraX version: 0.9 (2019-03-25)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
open "/Users/meng/Desktop/02-20-2000-522-26564/1-CTs from rtog conversion-564.2" format dicomTraceback (most recent call last):

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/ui/gui.py", line 808, in <lambda>

open_folder_action.triggered.connect(lambda arg, s=self, sess=session: s.folder_open_cb(sess))

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/ui/gui.py", line 573, in folder_open_cb

self._open_folder.display(session)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/ui/open_folder.py", line 62, in display

run(session, cmd)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run

results = command.run(text, log=log)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2616, in run

result = ci.function(session, kw_args)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 41, in open

from_database=from_database, ignore_cache=ignore_cache, kw))

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 117, in open

models = handle_unknown_kw(session.models.open, paths, format=format, name=name, kw)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw

return f(*args, kw)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/models.py", line 598, in open

session, filenames, format=format, name=name, kw)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/io.py", line 463, in open_multiple_data

models, status = open_func(session, paths, mname, kw)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom.py", line 39, in open_dicom

models, msg = dicom_volumes(session, image_series, kw)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom.py", line 117, in dicom_volumes

gmodels, gmsg = open_grids(session, grid_group, gname, kw)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py", line 3241, in open_grids

v.initialize_thresholds()

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py", line 520, in initialize_thresholds

s = self.matrix_value_statistics()

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py", line 1629, in matrix_value_statistics

matrices = self.displayed_matrices(read_matrix)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py", line 1664, in displayed_matrices

matrices.append(self.matrix(read_matrix))

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py", line 1179, in matrix

m = self.region_matrix(r, read_matrix)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py", line 1203, in region_matrix

m = d.matrix(origin, size, step, progress, from_cache_only)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/griddata.py", line 248, in matrix

m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/griddata.py", line 267, in read_matrix

m = self._read_full_planes(ijk_origin, ijk_size, ijk_step, progress)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/griddata.py", line 296, in _read_full_planes

m2d= self.read_xy_plane(k)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom_grid.py", line 118, in read_xy_plane

m = self.dicom_data.read_plane(k, self.time, c)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom_format.py", line 546, in read_plane

data *= self.rescale_slope

TypeError: Cannot cast ufunc multiply output from dtype('float64') to dtype('uint16') with casting rule 'same_kind'

TypeError: Cannot cast ufunc multiply output from dtype('float64') to dtype('uint16') with casting rule 'same_kind'

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom_format.py", line 546, in read_plane
data *= self.rescale_slope

See log for complete Python traceback.

Traceback (most recent call last):

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/triggerset.py", line 130, in invoke

return self._func(self._name, data)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py", line 3489, in _update_drawings

v.initialize_thresholds()

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py", line 520, in initialize_thresholds

s = self.matrix_value_statistics()

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py", line 1629, in matrix_value_statistics

matrices = self.displayed_matrices(read_matrix)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py", line 1664, in displayed_matrices

matrices.append(self.matrix(read_matrix))

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py", line 1179, in matrix

m = self.region_matrix(r, read_matrix)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py", line 1203, in region_matrix

m = d.matrix(origin, size, step, progress, from_cache_only)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/griddata.py", line 248, in matrix

m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/griddata.py", line 267, in read_matrix

m = self._read_full_planes(ijk_origin, ijk_size, ijk_step, progress)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/griddata.py", line 296, in _read_full_planes

m2d= self.read_xy_plane(k)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom_grid.py", line 118, in read_xy_plane

m = self.dicom_data.read_plane(k, self.time, c)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom_format.py", line 546, in read_plane

data *= self.rescale_slope

TypeError: Cannot cast ufunc multiply output from dtype('float64') to dtype('uint16') with casting rule 'same_kind'

Error processing trigger "graphics update": Cannot cast ufunc multiply output from dtype('float64') to dtype('uint16') with casting rule 'same_kind':
TypeError: Cannot cast ufunc multiply output from dtype('float64') to dtype('uint16') with casting rule 'same_kind'

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/dicom/dicom_format.py", line 546, in read_plane
data *= self.rescale_slope

See log for complete Python traceback.

[Elaine Meng]

I also get this error with the mouse brain MR, including the time series, but not the prostate time series on the 3DSlicer website (both mentioned on our examples page
​http://www.rbvi.ucsf.edu/chimerax/dicom/examples.html )

[Elaine Meng]

I get a similar error except for "ufunc add" instead of "ufunc multiply" trying to open the near-isotropic CT dataset mentioned on our examples page <​http://www.rbvi.ucsf.edu/chimerax/dicom/examples.html>:
TypeError: Cannot cast ufunc add output from dtype('int32') to dtype('uint16') with casting rule 'same_kind'

[Tom Goddard]

Fixed.

Problem was with floating point dicom scaling factor applied to integer value data in new plane reading code. Only tested first dataset mentioned since UCSF internet connectivity broken today.

[Elaine Meng]

I tested the datasets in the additional comments, and they all open without ufunc errors. Looks good, thanks!