id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1600 Reading map: 'numpy.float64' object cannot be interpreted as an integer Elaine Meng Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-01-10) Description tried to use ""move planes"" mouse mode after choosing ""orthoplanes"" display in Volume Viewer Log: UCSF ChimeraX version: 0.9 (2019-01-10) How to cite UCSF ChimeraX > open ""/Users/meng/Desktop/dicom/tcia/RIDER Lung CT/RIDER-1129164940/11-06-2014-1-96508/4-24533/*.dcm"" verbose true Summary of feedback from opening files --- notes | Data set: /Users/meng/Desktop/dicom/tcia/RIDER Lung CT/RIDER-1129164940/11-06-2014-1-96508/4-24533/000080.dcm (0008, 0000) Group Length UL: 280 (0008, 0005) Specific Character Set CS: 'ISO_IR 100' (0008, 0008) Image Type CS: ['ORIGINAL', 'PRIMARY', 'AXIAL'] (0008, 0012) Instance Creation Date DA: '20060920' (0008, 0013) Instance Creation Time TM: '093833' (0008, 0016) SOP Class UID UI: CT Image Storage (0008, 0018) SOP Instance UID UI: 1.3.6.1.4.1.9328.50.1.80864899926417612544734009966266898264 (0008, 0020) Study Date DA: '20060920' (0008, 0023) Content Date DA: '20060920' (0008, 0030) Study Time TM: '' (0008, 0033) Content Time TM: '' (0008, 0050) Accession Number SH: '1542750798412803' (0008, 0060) Modality CS: 'CT' (0008, 0070) Manufacturer LO: '' (0008, 0090) Referring Physician's Name PN: ' ' (0010, 0000) Group Length UL: 62 (0010, 0010) Patient's Name PN: '296698' (0010, 0020) Patient ID LO: 'RIDER-1129164940' (0010, 0030) Patient's Birth Date DA: '19461119' (0010, 0040) Patient's Sex CS: '' (0012, 0000) Group Length UL: 62 (0012, 0062) Patient Identity Removed CS: 'YES' (0012, 0063) De-identification Method LO: 'CTP: DICOM-S142-Baseline: 20090626:165427' (0013, 0000) Private Creator UN: b'2\x00\x00\x00' (0013, 0010) Private tag data LO: 'CTP' (0013, 1010) Private tag data UN: b'RIDER Lung CT\x00' (0013, 1013) Private tag data UN: b'92033002' (0018, 0000) Group Length UL: 390 (0018, 0010) Contrast/Bolus Agent LO: '' (0018, 0015) Body Part Examined CS: 'CHEST' (0018, 0022) Scan Options CS: 'HELICAL MODE' (0018, 0050) Slice Thickness DS: ""1.250000"" (0018, 0060) KVP DS: ""120"" (0018, 0090) Data Collection Diameter DS: ""500.000000"" (0018, 1100) Reconstruction Diameter DS: ""295.000000"" (0018, 1110) Distance Source to Detector DS: ""949.075012"" (0018, 1111) Distance Source to Patient DS: ""541.000000"" (0018, 1120) Gantry/Detector Tilt DS: ""0.000000"" (0018, 1130) Table Height DS: ""127.400002"" (0018, 1140) Rotation Direction CS: 'CW' (0018, 1150) Exposure Time IS: ""505"" (0018, 1151) X-Ray Tube Current IS: ""399"" (0018, 1152) Exposure IS: ""9"" (0018, 1160) Filter Type SH: 'BODY FILTER' (0018, 1170) Generator Power IS: ""48000"" (0018, 1190) Focal Spot(s) DS: ""1.200000"" (0018, 1210) Convolution Kernel SH: 'LUNG' (0018, 5100) Patient Position CS: 'FFS' (0018, 9305) Revolution Time FD: 0.5 (0018, 9306) Single Collimation Width FD: 1.25 (0018, 9307) Total Collimation Width FD: 20.0 (0018, 9309) Table Speed FD: 55.0 (0018, 9310) Table Feed per Rotation FD: 27.5 (0018, 9311) Spiral Pitch Factor FD: 1.375 (0020, 0000) Group Length UL: 378 (0020, 000d) Study Instance UID UI: 1.3.6.1.4.1.9328.50.1.216116555221814778114703363464001196508 (0020, 000e) Series Instance UID UI: 1.3.6.1.4.1.9328.50.1.83304264089411327530730818890072724533 (0020, 0010) Study ID SH: '' (0020, 0011) Series Number IS: ""4"" (0020, 0012) Acquisition Number IS: ""1"" (0020, 0013) Instance Number IS: ""2"" (0020, 0032) Image Position (Patient) DS: ['-146.699997', '-155.300003', '-36.250000'] (0020, 0037) Image Orientation (Patient) DS: ['1.000000', '0.000000', '0.000000', '0.000000', '1.000000', '0.000000'] (0020, 0052) Frame of Reference UID UI: 1.3.6.1.4.1.9328.50.1.223115801243567643226232109211259092756 (0020, 1040) Position Reference Indicator LO: 'SN' (0020, 1041) Slice Location DS: ""-36.250000"" (0028, 0000) Group Length UL: 182 (0028, 0002) Samples per Pixel US: 1 (0028, 0004) Photometric Interpretation CS: 'MONOCHROME2' (0028, 0010) Rows US: 512 (0028, 0011) Columns US: 512 (0028, 0030) Pixel Spacing DS: ['0.576172', '0.576172'] (0028, 0100) Bits Allocated US: 16 (0028, 0101) Bits Stored US: 16 (0028, 0102) High Bit US: 15 (0028, 0103) Pixel Representation US: 1 (0028, 0120) Pixel Padding Value SS: -2000 (0028, 1050) Window Center DS: ""40"" (0028, 1051) Window Width DS: ""400"" (0028, 1052) Rescale Intercept DS: ""-1024"" (0028, 1053) Rescale Slope DS: ""1"" (0028, 1054) Rescale Type LO: 'HU' (0040, 0000) Group Length UL: 30 (0040, 0244) Performed Procedure Step Start Date DA: '20060920' (0040, 0245) Performed Procedure Step Start Time TM: '093136' (7fe0, 0010) Pixel Data OW: Array of 524288 bytes Opened RIDE 20060920, grid size 512,512,236, pixel 0.576,0.576,1.25, shown at step 1, values int16 > ui mousemode rightMode move planes Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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/3.6/lib/python3.6/site- packages/chimerax/map/volume.py"", line 3383, in _update_drawings v.update_drawings() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/volume.py"", line 659, in update_drawings self._keep_displayed_data = self.displayed_matrices() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/volume.py"", line 1592, in displayed_matrices matrices.append(self.matrix_plane(axis, omijk[axis], read_matrix)) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/volume.py"", line 1185, in matrix_plane m = self.region_matrix((ijk_min, ijk_max, ijk_step), read_matrix) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/volume.py"", line 1134, 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/3.6/lib/python3.6/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/3.6/lib/python3.6/site- packages/chimerax/map/data/dicom/dicom_grid.py"", line 59, in read_matrix m = allocate_array(ijk_size, self.value_type, ijk_step, progress) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/data/readarray.py"", line 203, in allocate_array m = alloc(shape, value_type) TypeError: 'numpy.float64' object cannot be interpreted as an integer Error processing trigger ""graphics update"": 'numpy.float64' object cannot be interpreted as an integer: TypeError: 'numpy.float64' object cannot be interpreted as an integer File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/data/readarray.py"", line 203, in allocate_array m = alloc(shape, value_type) See log for complete Python traceback. An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/updateloop.py"", line 72, in draw_new_frame view.draw(check_for_changes = False) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/view.py"", line 159, in draw self._draw_scene(camera, drawings) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/view.py"", line 217, in _draw_scene draw_opaque(r, opaque_drawings) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 1360, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 1371, in _draw_multiple d.draw(renderer, draw_pass) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/grayscale.py"", line 237, in draw pd = self.make_planes(axis) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/grayscale.py"", line 298, in make_planes d = self.make_ortho_planes() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/grayscale.py"", line 340, in make_ortho_planes d = self.make_planes_drawing(planes) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/grayscale.py"", line 373, in make_planes_drawing textures.append(self.texture_plane(k, axis)) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/grayscale.py"", line 391, in texture_plane d = self.color_plane(k, axis) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/grayscale.py"", line 409, in color_plane p = self.get_color_plane(axis, k) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/solid.py"", line 211, in get_color_plane return self.color_values(axis, plane, cmap, cmap_range) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/solid.py"", line 228, in color_values m = self.matrix_plane(axis, plane) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/volume.py"", line 1185, in matrix_plane m = self.region_matrix((ijk_min, ijk_max, ijk_step), read_matrix) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/volume.py"", line 1134, 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/3.6/lib/python3.6/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/3.6/lib/python3.6/site- packages/chimerax/map/data/dicom/dicom_grid.py"", line 59, in read_matrix m = allocate_array(ijk_size, self.value_type, ijk_step, progress) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/data/readarray.py"", line 203, in allocate_array m = alloc(shape, value_type) TypeError: 'numpy.float64' object cannot be interpreted as an integer OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Volume Data fixed all ChimeraX