Warning: I have a complete lack of understanding of how mrc files are read/written. I also understand that the plugin is in development!
ValueError Traceback (most recent call last)
File src/psygnal/_signal.py:912, in psygnal._signal.SignalInstance._run_emit_loop()
File ~/miniconda3/envs/blik/lib/python3.9/site-packages/magicgui/widgets/_function_gui.py:207, in FunctionGui.__init__.<locals>._disable_button_and_call()
206 try:
--> 207 self.__call__()
self = <FunctionGui file_reader(files: List[pathlib.Path] = (PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc'),), name_regex: List[str] = [], names: List[str] = [], as_dask_array: bool = True) -> <function NewType.<locals>.new_type at 0x7f376cfd7f70>>
208 finally:
File ~/miniconda3/envs/blik/lib/python3.9/site-packages/magicgui/widgets/_function_gui.py:318, in FunctionGui.__call__(self=<FunctionGui file_reader(files: List[pathlib.Pat... = True) -> <function NewType.<locals>.new_type>>, update_widget=False, *args=(), **kwargs={})
317 with _function_name_pointing_to_widget(self):
--> 318 value = self._function(*bound.args, **bound.kwargs)
self = <FunctionGui file_reader(files: List[pathlib.Path] = (PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc'),), name_regex: List[str] = [], names: List[str] = [], as_dask_array: bool = True) -> <function NewType.<locals>.new_type at 0x7f376cfd7f70>>
bound = <BoundArguments (files=(PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc'),), name_regex=[], names=[], as_dask_array=True)>
self._function = <function file_reader at 0x7f36fcc02670>
320 self._call_count += 1
File ~/miniconda3/envs/blik/lib/python3.9/site-packages/blik/widgets/file_reader.py:29, in file_reader(files=(PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc'),), name_regex=[], names=[], as_dask_array=True)
23 """
24 Read files with blik.
25
26 name_regex: a regex string. Matching text will be used as name for the piece of data
27 names: only load data matching this comma separated list of names
28 """
---> 29 return read_layers(*files, name_regex=name_regex or None, names=names or None, lazy=as_dask_array)
files = (PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc'),)
name_regex or None = None
names or None = None
as_dask_array = True
name_regex = []
names = []
File ~/miniconda3/envs/blik/lib/python3.9/site-packages/blik/reader.py:73, in read_layers(*paths=(PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc'),), **kwargs={'lazy': True, 'name_regex': None, 'names': None})
72 def read_layers(*paths, **kwargs):
---> 73 data_list = read(*paths, **kwargs)
paths = (PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc'),)
kwargs = {'name_regex': None, 'names': None, 'lazy': True}
74 layers = []
File ~/miniconda3/envs/blik/lib/python3.9/site-packages/naaf/reading/main.py:76, in read(name_regex=None, names=None, strict=False, lazy=True, *paths=(PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc'),), **kwargs={})
75 try:
---> 76 data.extend(read_file(file, name_regex=name_regex, lazy=lazy, **kwargs))
data = []
file = PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc')
name_regex = None
lazy = True
kwargs = {}
77 except ParseError:
File ~/miniconda3/envs/blik/lib/python3.9/site-packages/naaf/reading/main.py:35, in read_file(file_path=PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc'), **kwargs={'lazy': True, 'name_regex': None})
34 try:
---> 35 data = listify(func(file_path, **kwargs))
func = <function read_mrc at 0x7f36fc695790>
file_path = PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc')
kwargs = {'name_regex': None, 'lazy': True}
36 for d in data:
File ~/miniconda3/envs/blik/lib/python3.9/site-packages/naaf/reading/mrc.py:16, in read_mrc(image_path=PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc'), name_regex=None, lazy=True, **kwargs={})
14 name = guess_name(image_path, name_regex)
---> 16 with mrcfile.mmap(image_path) as mrc:
image_path = PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc')
17 if lazy:
File ~/miniconda3/envs/blik/lib/python3.9/site-packages/mrcfile/load_functions.py:208, in mmap(name=PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc'), mode='r', permissive=False)
185 """Open a memory-mapped MRC file.
186
187 This allows much faster opening of large files, because the data is only
(...)
206 An :class:`~mrcfile.mrcmemmap.MrcMemmap` object.
207 """
--> 208 return MrcMemmap(name, mode=mode, permissive=permissive)
name = PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc')
mode = 'r'
permissive = False
File ~/miniconda3/envs/blik/lib/python3.9/site-packages/mrcfile/mrcfile.py:114, in MrcFile.__init__(self=MrcMemmap('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc', mode='r'), name=PosixPath('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc'), mode='r', overwrite=False, permissive=False, header_only=False, **kwargs={})
113 else:
--> 114 self._read(header_only)
self = MrcMemmap('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc', mode='r')
header_only = False
115 except Exception:
File ~/miniconda3/envs/blik/lib/python3.9/site-packages/mrcfile/mrcfile.py:130, in MrcFile._read(self=MrcMemmap('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc', mode='r'), header_only=False)
129 self._iostream.seek(0)
--> 130 super(MrcFile, self)._read(header_only)
header_only = False
self = MrcMemmap('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc', mode='r')
132 # Check if the file is the expected size.
File ~/miniconda3/envs/blik/lib/python3.9/site-packages/mrcfile/mrcinterpreter.py:173, in MrcInterpreter._read(self=MrcMemmap('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc', mode='r'), header_only=False)
154 """Read the header, extended header and data from the I/O stream.
155
156 Before calling this method, the stream should be open and positioned at
(...)
171 as a valid MRC file and ``permissive`` is :data:`True`.
172 """
--> 173 self._read_header()
self = MrcMemmap('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc', mode='r')
174 self._read_extended_header()
File ~/miniconda3/envs/blik/lib/python3.9/site-packages/mrcfile/mrcinterpreter.py:215, in MrcInterpreter._read_header(self=MrcMemmap('/home/joran.deschamps/Desktop/projects/Helen/blik/21.mrc', mode='r'))
214 try:
--> 215 byte_order = utils.byte_order_from_machine_stamp(header.machst)
header = rec.array((1024, 1024, 512, 2, 0, 0, 0, 1024, 1024, 512, (1024., 1024., 512.), (90., 90., 90.), 1, 2, 3, -995.9688, 480.2282, -2.2351742e-07, 0, 0, b'\x00\x00\x00\x00\x00\x00\x00\x00', b'', 0, b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00', (0., 0., 0.), b'MAP ', [68, 32, 32, 32], -1., 0, [b'', b'', b'', b'', b'', b'', b'', b'', b'', b'']),
dtype=[('nx', '<i4'), ('ny', '<i4'), ('nz', '<i4'), ('mode', '<i4'), ('nxstart', '<i4'), ('nystart', '<i4'), ('nzstart', '<i4'), ('mx', '<i4'), ('my', '<i4'), ('mz', '<i4'), ('cella', [('x', '<f4'), ('y', '<f4'), ('z', '<f4')]), ('cellb', [('alpha', '<f4'), ('beta', '<f4'), ('gamma', '<f4')]), ('mapc', '<i4'), ('mapr', '<i4'), ('maps', '<i4'), ('dmin', '<f4'), ('dmax', '<f4'), ('dmean', '<f4'), ('ispg', '<i4'), ('nsymbt', '<i4'), ('extra1', 'V8'), ('exttyp', 'S4'), ('nversion', '<i4'), ('extra2', 'V84'), ('origin', [('x', '<f4'), ('y', '<f4'), ('z', '<f4')]), ('map', 'S4'), ('machst', 'u1', (4,)), ('rms', '<f4'), ('nlabl', '<i4'), ('label', 'S80', (10,))])
utils = <module 'mrcfile.utils' from '/home/joran.deschamps/miniconda3/envs/blik/lib/python3.9/site-packages/mrcfile/utils.py'>
216 except ValueError as err:
File ~/miniconda3/envs/blik/lib/python3.9/site-packages/mrcfile/utils.py:199, in byte_order_from_machine_stamp(machst=<class 'numpy.ndarray'> (4,) uint8)
198 pretty_bytes = pretty_machine_stamp(machst)
--> 199 raise ValueError("Unrecognised machine stamp: " + pretty_bytes)
pretty_bytes = '0x44 0x20 0x20 0x20'
"Unrecognised machine stamp: " + pretty_bytes = 'Unrecognised machine stamp: 0x44 0x20 0x20 0x20'
ValueError: Unrecognised machine stamp: 0x44 0x20 0x20 0x20
The above exception was the direct cause of the following exception:
EmitLoopError Traceback (most recent call last)
File ~/miniconda3/envs/blik/lib/python3.9/site-packages/magicgui/widgets/_bases/value_widget.py:57, in ValueWidget._on_value_change(self=PushButton(value=False, annotation=None, name='call_button'), value=False)
55 if value is self.null_value and not self._nullable:
56 return
---> 57 self.changed.emit(value)
value = False
self.changed = <SignalInstance 'changed' on PushButton(value=False, annotation=None, name='call_button')>
self = PushButton(value=False, annotation=None, name='call_button')
File src/psygnal/_signal.py:849, in psygnal._signal.SignalInstance.emit()
File src/psygnal/_signal.py:891, in psygnal._signal.SignalInstance._run_emit_loop()
File src/psygnal/_signal.py:892, in psygnal._signal.SignalInstance._run_emit_loop()
File src/psygnal/_signal.py:914, in psygnal._signal.SignalInstance._run_emit_loop()
EmitLoopError: calling <function FunctionGui.__init__.<locals>._disable_button_and_call at 0x7f36fc5c7790> with args=() caused ValueError in emit loop.
^CTraceback (most recent call last):
File "/home/joran.deschamps/miniconda3/envs/blik/bin/napari", line 8, in <module>
sys.exit(main())
File "/home/joran.deschamps/miniconda3/envs/blik/lib/python3.9/site-packages/napari/__main__.py", line 447, in main
_run()
File "/home/joran.deschamps/miniconda3/envs/blik/lib/python3.9/site-packages/napari/__main__.py", line 336, in _run
run(gui_exceptions=True)
File "/home/joran.deschamps/miniconda3/envs/blik/lib/python3.9/site-packages/napari/_qt/qt_event_loop.py", line 402, in run
app.exec_()
File "/home/joran.deschamps/miniconda3/envs/blik/lib/python3.9/contextlib.py", line 126, in __exit__
next(self.gen)
File "/home/joran.deschamps/miniconda3/envs/blik/lib/python3.9/site-packages/napari/_qt/utils.py", line 459, in _maybe_allow_interrupt
old_sigint_handler(*handler_args)
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