id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
3993	issue with AtomicShapeDrawing.add_shape	Tony Schaefer	Greg Couch	"{{{
I cannot add a shape to a chimerax.atomic.AtomicShapeDrawing when the 'color' argument is either an N x 4 numpy array or a list

if it's a numpy array (first two times I ran my python script), it fails because numpy arrays don't have an 'asarray' method

if it's a list (last time I ran the script), it fails because lists don't have the 'ndim' attribute


Log:
cd C:\Users\normn/Desktop
Current working directory is: C:\Users\normn\Desktop
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
open C:\Users\normn\Desktop\test_triangles.py format python
spend 0.29s figuring out which points to delete
spend 3.72s deleting points and triangles
spend 0.02s shifting indicis for triangles
Traceback (most recent call last):
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py"", line 629, in customEvent
    func(*args, **kw)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py"", line 440, in defer
    cxcmd(session, topic)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py"", line 456, in cxcmd
    run(session, cmd)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\run.py"", line 31, in run
    results = command.run(text, log=log)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2805, in run
    result = ci.function(session, **kw_args)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py"", line 100, in cmd_open
    return Command(session, registry=registry).run(provider_cmd_text, log=log)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2805, in run
    result = ci.function(session, **kw_args)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py"", line 154, in provider_open
    name or model_name_from_path(fi.file_name)), provider_kw)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py"", line 372, in collated_open
    return func(*func_args, **func_kw)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core_formats\__init__.py"", line 48, in open
    return open_python_script(session, data, file_name)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\scripting.py"", line 82, in open_python_script
    _exec_python(session, code, argv)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\scripting.py"", line 59, in _exec_python
    exec(code, sandbox.__dict__)
  File ""test_triangles.py"", line 169, in <module>
    drawing.add_shape(c_v, c_n, new_t, colors)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\atomic\shapedrawing.py"", line 221, in add_shape
    colors = color.asarray(color, dtype=numpy.uint8)
AttributeError: 'numpy.ndarray' object has no attribute 'asarray'

AttributeError: 'numpy.ndarray' object has no attribute 'asarray'

File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\atomic\shapedrawing.py"", line 221, in add_shape
colors = color.asarray(color, dtype=numpy.uint8)

See log for complete Python traceback.

ui tool show Shell
open C:\Users\normn\Desktop\test_triangles.py format python
spend 0.28s figuring out which points to delete
spend 3.72s deleting points and triangles
spend 0.02s shifting indicis for triangles
colors shape: (3386, 4)
Traceback (most recent call last):
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py"", line 629, in customEvent
    func(*args, **kw)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py"", line 440, in defer
    cxcmd(session, topic)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py"", line 456, in cxcmd
    run(session, cmd)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\run.py"", line 31, in run
    results = command.run(text, log=log)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2805, in run
    result = ci.function(session, **kw_args)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py"", line 100, in cmd_open
    return Command(session, registry=registry).run(provider_cmd_text, log=log)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2805, in run
    result = ci.function(session, **kw_args)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py"", line 154, in provider_open
    name or model_name_from_path(fi.file_name)), provider_kw)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py"", line 372, in collated_open
    return func(*func_args, **func_kw)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core_formats\__init__.py"", line 48, in open
    return open_python_script(session, data, file_name)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\scripting.py"", line 82, in open_python_script
    _exec_python(session, code, argv)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\scripting.py"", line 59, in _exec_python
    exec(code, sandbox.__dict__)
  File ""test_triangles.py"", line 169, in <module>
    drawing.add_shape(c_v, c_n, new_t, colors)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\atomic\shapedrawing.py"", line 221, in add_shape
    colors = color.asarray(color, dtype=numpy.uint8)
AttributeError: 'numpy.ndarray' object has no attribute 'asarray'

AttributeError: 'numpy.ndarray' object has no attribute 'asarray'

File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\atomic\shapedrawing.py"", line 221, in add_shape
colors = color.asarray(color, dtype=numpy.uint8)

See log for complete Python traceback.

open C:\Users\normn\Desktop\test_triangles.py format python
spend 0.28s figuring out which points to delete
spend 3.71s deleting points and triangles
spend 0.02s shifting indicis for triangles
colors shape: (3386, 4)
Traceback (most recent call last):
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py"", line 629, in customEvent
    func(*args, **kw)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py"", line 440, in defer
    cxcmd(session, topic)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py"", line 456, in cxcmd
    run(session, cmd)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\run.py"", line 31, in run
    results = command.run(text, log=log)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2805, in run
    result = ci.function(session, **kw_args)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py"", line 100, in cmd_open
    return Command(session, registry=registry).run(provider_cmd_text, log=log)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2805, in run
    result = ci.function(session, **kw_args)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py"", line 154, in provider_open
    name or model_name_from_path(fi.file_name)), provider_kw)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py"", line 372, in collated_open
    return func(*func_args, **func_kw)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core_formats\__init__.py"", line 48, in open
    return open_python_script(session, data, file_name)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\scripting.py"", line 82, in open_python_script
    _exec_python(session, code, argv)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\scripting.py"", line 59, in _exec_python
    exec(code, sandbox.__dict__)
  File ""test_triangles.py"", line 171, in <module>
    drawing.add_shape(c_v, c_n, new_t, colors)
  File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\atomic\shapedrawing.py"", line 217, in add_shape
    if color.ndim == 1 or color.shape[0] == 1:
AttributeError: 'list' object has no attribute 'ndim'

AttributeError: 'list' object has no attribute 'ndim'

File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\atomic\shapedrawing.py"", line 217, in add_shape
if color.ndim == 1 or color.shape[0] == 1:

See log for complete Python traceback.

Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\bug_reporter\bug_reporter_gui.py"", line 241, in submit
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST, BUG_SELECTOR, fields)
File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\webservices\post_form.py"", line 40, in post_multipart_formdata
h.request('POST', url, body=body, headers=headers)
File ""D:\ChimeraX 1.1\bin\lib\http\client.py"", line 1262, in request
self._send_request(method, url, body, headers, encode_chunked)
File ""D:\ChimeraX 1.1\bin\lib\http\client.py"", line 1308, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File ""D:\ChimeraX 1.1\bin\lib\http\client.py"", line 1257, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File ""D:\ChimeraX 1.1\bin\lib\http\client.py"", line 1028, in _send_output
self.send(msg)
File ""D:\ChimeraX 1.1\bin\lib\http\client.py"", line 968, in send
self.connect()
File ""D:\ChimeraX 1.1\bin\lib\http\client.py"", line 940, in connect
(self.host,self.port), self.timeout, self.source_address)
File ""D:\ChimeraX 1.1\bin\lib\socket.py"", line 728, in create_connection
raise err
File ""D:\ChimeraX 1.1\bin\lib\socket.py"", line 716, in create_connection
sock.connect(sa)
TimeoutError: [WinError 10060] A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond
Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\bug_reporter\bug_reporter_gui.py"", line 241, in submit
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST, BUG_SELECTOR, fields)
File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\webservices\post_form.py"", line 40, in post_multipart_formdata
h.request('POST', url, body=body, headers=headers)
File ""D:\ChimeraX 1.1\bin\lib\http\client.py"", line 1262, in request
self._send_request(method, url, body, headers, encode_chunked)
File ""D:\ChimeraX 1.1\bin\lib\http\client.py"", line 1308, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File ""D:\ChimeraX 1.1\bin\lib\http\client.py"", line 1257, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File ""D:\ChimeraX 1.1\bin\lib\http\client.py"", line 1028, in _send_output
self.send(msg)
File ""D:\ChimeraX 1.1\bin\lib\http\client.py"", line 968, in send
self.connect()
File ""D:\ChimeraX 1.1\bin\lib\http\client.py"", line 940, in connect
(self.host,self.port), self.timeout, self.source_address)
File ""D:\ChimeraX 1.1\bin\lib\socket.py"", line 728, in create_connection
raise err
File ""D:\ChimeraX 1.1\bin\lib\socket.py"", line 716, in create_connection
sock.connect(sa)
TimeoutError: [WinError 10060] A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond

}}}
"	defect	closed	normal		Graphics		fixed		Tom Goddard				all	ChimeraX