id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1745 Error opening DICOM with lossless JPEG image encoding goddard@… Zach Pearson "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-02-19) Description Opening the attached DICOM file with lossless JPEG image encoding gives this error. Log: UCSF ChimeraX version: 0.9 (2019-02-19) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/goddard/ucsf/data/dicom/02ef8f31ea86a45cfce6eb297c274598/series-000001/image-000001.dcm Traceback (most recent call last): File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pydicom/pixel_data_handlers/pillow_handler.py"", line 197, in get_pixeldata decompressed_image = Image.open(fio) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/PIL/Image.py"", line 2687, in open % (filename if filename else fp)) OSError: cannot identify image file <_io.BytesIO object at 0x13d5254c0> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 252, in execute cmd.run(cmd_text) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2617, in run result = ci.function(session, **kw_args) File ""/Users/goddard/Desktop/ChimeraX.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/goddard/Desktop/ChimeraX.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/goddard/Desktop/ChimeraX.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/goddard/Desktop/ChimeraX.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/goddard/Desktop/ChimeraX.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/goddard/Desktop/ChimeraX.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/goddard/Desktop/ChimeraX.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/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 3222, in open_grids v.initialize_thresholds() File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 518, in initialize_thresholds s = self.matrix_value_statistics() File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1613, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1648, in displayed_matrices matrices.append(self.matrix(read_matrix)) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1163, in matrix m = self.region_matrix(r, read_matrix) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1187, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/griddata.py"", line 249, in matrix m = self._read_full_planes(ijk_origin, ijk_size, ijk_step, progress) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/griddata.py"", line 274, in _read_full_planes fm = self.read_matrix(f_ijk_origin, f_ijk_size, f_ijk_step, progress) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/dicom/dicom_grid.py"", line 117, in read_matrix self.time, c, m, progress) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/dicom/dicom_format.py"", line 523, in read_matrix p = self.read_plane(k, time, channel) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/dicom/dicom_format.py"", line 541, in read_plane data = d.pixel_array File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pydicom/dataset.py"", line 929, in pixel_array self.convert_pixel_data() File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pydicom/dataset.py"", line 875, in convert_pixel_data raise last_exception File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pydicom/dataset.py"", line 843, in convert_pixel_data arr = handler.get_pixeldata(self) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pydicom/pixel_data_handlers/pillow_handler.py"", line 199, in get_pixeldata raise NotImplementedError(e.strerror) NotImplementedError: None NotImplementedError: None File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pydicom/pixel_data_handlers/pillow_handler.py"", line 199, in get_pixeldata raise NotImplementedError(e.strerror) See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pydicom/pixel_data_handlers/pillow_handler.py"", line 197, in get_pixeldata decompressed_image = Image.open(fio) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/PIL/Image.py"", line 2687, in open % (filename if filename else fp)) OSError: cannot identify image file <_io.BytesIO object at 0x13d5c0990> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Users/goddard/Desktop/ChimeraX.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/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 3470, in _update_drawings v.initialize_thresholds() File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 518, in initialize_thresholds s = self.matrix_value_statistics() File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1613, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1648, in displayed_matrices matrices.append(self.matrix(read_matrix)) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1163, in matrix m = self.region_matrix(r, read_matrix) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1187, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/griddata.py"", line 249, in matrix m = self._read_full_planes(ijk_origin, ijk_size, ijk_step, progress) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/griddata.py"", line 274, in _read_full_planes fm = self.read_matrix(f_ijk_origin, f_ijk_size, f_ijk_step, progress) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/dicom/dicom_grid.py"", line 117, in read_matrix self.time, c, m, progress) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/dicom/dicom_format.py"", line 523, in read_matrix p = self.read_plane(k, time, channel) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/dicom/dicom_format.py"", line 541, in read_plane data = d.pixel_array File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pydicom/dataset.py"", line 929, in pixel_array self.convert_pixel_data() File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pydicom/dataset.py"", line 875, in convert_pixel_data raise last_exception File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pydicom/dataset.py"", line 843, in convert_pixel_data arr = handler.get_pixeldata(self) File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pydicom/pixel_data_handlers/pillow_handler.py"", line 199, in get_pixeldata raise NotImplementedError(e.strerror) NotImplementedError: None Error processing trigger ""graphics update"": None: NotImplementedError: None File ""/Users/goddard/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pydicom/pixel_data_handlers/pillow_handler.py"", line 199, in get_pixeldata raise NotImplementedError(e.strerror) See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 680MX OpenGL Engine OpenGL vendor: NVIDIA Corporation File attachment: image-000001.dcm }}} [attachment:""image-000001.dcm""] " enhancement closed normal DICOM wontfix Eric Pettersen Greg Couch all ChimeraX