import of flucam image emi file yields empty list #70
Labels
type: bug
Something isn't working
Comments
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Update: I've done a bit of digging and it turns out that flu cam emi files are somewhat unusual: there's almost no metadata and the structure is very different to standard TEM images. It might be too much of an edge case for hyperspy's developers to spend much time on so am happy for this issue to be closed. |
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I transfered this issue to hyperspy/rosettasciio as the development of IO code will now take place here. I guess it shouldn't be that difficult to figure out and it would be useful to be read images acquired with the flu cam. |
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Describe the bug
Using hs.load to load a emi file of a flucam image yields an empty list []. I have checked that normal TEM images (ie. from a proper camera) work properly. Note that flucam images only save .emi files, not a complimentary ser file.
To Reproduce
Example file:
Spotsize3GL6.zip
$ conda activate hyperspy
$ ipython
In [1]: import hyperspy.api as hs
In [2]: hs.load('Spotsize3GL6.emi')
Out[2]: []
Expected behavior
Object returned by hs.load should contain image and metadata (just pixel size in this instance)
Python environement:
Latest version of hyperspy as installed through conda
$ python --version
Python 3.10.6
$ conda env export
name: hyperspy
channels:
conda-forge
defaults
dependencies:
_libgcc_mutex=0.1=conda_forge
_openmp_mutex=4.5=2_gnu
alsa-lib=1.2.7.2=h166bdaf_0
aom=3.5.0=h27087fc_0
asciitree=0.3.3=py_2
asttokens=2.0.8=pyhd8ed1ab_0
attr=2.5.1=h166bdaf_1
attrs=22.1.0=pyh71513ae_1
backcall=0.2.0=pyh9f0ad1d_0
backports=1.0=py_2
backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
bokeh=2.4.3=pyhd8ed1ab_3
brotli=1.0.9=h166bdaf_7
brotli-bin=1.0.9=h166bdaf_7
brunsli=0.1=h9c3ff4c_0
bzip2=1.0.8=h7f98852_4
c-ares=1.18.1=h7f98852_0
c-blosc2=2.4.2=h7a311fb_0
ca-certificates=2022.9.24=ha878542_0
cached-property=1.5.2=hd8ed1ab_1
cached_property=1.5.2=pyha770c72_1
certifi=2022.9.24=pyhd8ed1ab_0
cfitsio=4.1.0=hd9d235c_0
charls=2.3.4=h9c3ff4c_0
charset-normalizer=2.1.1=pyhd8ed1ab_0
click=8.1.3=unix_pyhd8ed1ab_2
cloudpickle=2.2.0=pyhd8ed1ab_0
colorama=0.4.5=pyhd8ed1ab_0
cycler=0.11.0=pyhd8ed1ab_0
dask=2022.2.1=pyhd3eb1b0_0
dask-core=2022.2.1=pyhd3eb1b0_0
dav1d=1.0.0=h166bdaf_1
dbus=1.13.6=h5008d03_3
decorator=5.1.1=pyhd8ed1ab_0
dill=0.3.5.1=pyhd8ed1ab_0
distributed=2022.2.1=pyhd3eb1b0_0
entrypoints=0.4=pyhd8ed1ab_0
executing=1.1.0=pyhd8ed1ab_0
expat=2.5.0=h27087fc_0
fasteners=0.17.3=pyhd8ed1ab_0
fftw=3.3.10=nompi_hf0379b8_105
font-ttf-dejavu-sans-mono=2.37=hab24e00_0
font-ttf-inconsolata=3.000=h77eed37_0
font-ttf-source-code-pro=2.038=h77eed37_0
font-ttf-ubuntu=0.83=hab24e00_0
fontconfig=2.14.1=hc2a2eb6_0
fonts-conda-ecosystem=1=0
fonts-conda-forge=1=0
freetype=2.12.1=hca18f0e_0
fsspec=2022.8.2=pyhd8ed1ab_0
gettext=0.21.1=h27087fc_0
giflib=5.2.1=h36c2ea0_2
glib=2.74.1=h6239696_0
glib-tools=2.74.1=h6239696_0
gmp=6.2.1=h58526e2_0
gst-plugins-base=1.20.3=h57caac4_2
gstreamer=1.20.3=hd4edc92_2
hdf5=1.12.2=nompi_h2386368_100
heapdict=1.0.1=py_0
hyperspy-base=1.7.3=py310h5764c6d_0
hyperspy-gui-ipywidgets=1.5.0=pyhd8ed1ab_0
hyperspy-gui-traitsui=1.5.2=pyhd8ed1ab_0
icu=70.1=h27087fc_0
idna=3.4=pyhd8ed1ab_0
imageio=2.22.0=pyhfa7a67d_0
importlib_metadata=4.11.4=hd8ed1ab_0
importlib_resources=5.10.0=pyhd8ed1ab_0
ipyfilechooser=0.6.0=pyhd8ed1ab_0
ipykernel=6.16.0=pyh210e3f2_0
ipyparallel=8.4.1=pyhd8ed1ab_0
ipython=8.5.0=pyh41d4057_1
ipywidgets=8.0.2=pyhd8ed1ab_1
jack=1.9.21=h2a1e645_0
jedi=0.18.1=pyhd8ed1ab_2
jinja2=3.1.2=pyhd8ed1ab_1
joblib=1.2.0=pyhd8ed1ab_0
jpeg=9e=h166bdaf_2
jsonschema=4.17.0=pyhd8ed1ab_0
jupyter_client=7.3.5=pyhd8ed1ab_0
jupyter_core=4.11.1=py310hff52083_0
jupyterlab_widgets=3.0.3=pyhd8ed1ab_0
jxrlib=1.1=h7f98852_2
keyutils=1.6.1=h166bdaf_0
krb5=1.19.3=h3790be6_0
lame=3.100=h166bdaf_1003
lcms2=2.12=hddcbb42_0
ld_impl_linux-64=2.36.1=hea4e1c9_2
lerc=4.0.0=h27087fc_0
libaec=1.0.6=h9c3ff4c_0
libavif=0.10.1=h5cdd6b5_2
libblas=3.9.0=16_linux64_openblas
libbrotlicommon=1.0.9=h166bdaf_7
libbrotlidec=1.0.9=h166bdaf_7
libbrotlienc=1.0.9=h166bdaf_7
libcap=2.66=ha37c62d_0
libcblas=3.9.0=16_linux64_openblas
libclang=14.0.6=default_hc1a23ef_0
libclang13=14.0.6=default_h31cde19_0
libcups=2.3.3=h3e49a29_2
libcurl=7.83.1=h7bff187_0
libdb=6.2.32=h9c3ff4c_0
libdeflate=1.14=h166bdaf_0
libedit=3.1.20191231=he28a2e2_2
libev=4.33=h516909a_1
libevent=2.1.10=h9b69904_4
libffi=3.4.2=h7f98852_5
libflac=1.4.2=h27087fc_0
libgcc-ng=12.1.0=h8d9b700_16
libgfortran-ng=12.1.0=h69a702a_16
libgfortran5=12.1.0=hdcd56e2_16
libglib=2.74.1=h7a41b64_0
libgomp=12.1.0=h8d9b700_16
libiconv=1.17=h166bdaf_0
liblapack=3.9.0=16_linux64_openblas
libllvm11=11.1.0=he0ac6c6_4
libllvm14=14.0.6=he0ac6c6_0
libnghttp2=1.47.0=hdcd2b5c_1
libnsl=2.0.0=h7f98852_0
libogg=1.3.4=h7f98852_1
libopenblas=0.3.21=pthreads_h78a6416_3
libopus=1.3.1=h7f98852_1
libpng=1.6.38=h753d276_0
libpq=14.5=hd77ab85_1
libsndfile=1.1.0=h27087fc_0
libsodium=1.0.18=h36c2ea0_1
libsqlite=3.39.3=h753d276_0
libssh2=1.10.0=haa6b8db_3
libstdcxx-ng=12.1.0=ha89aaad_16
libtiff=4.4.0=h55922b4_4
libtool=2.4.6=h9c3ff4c_1008
libudev1=252=h166bdaf_0
libuuid=2.32.1=h7f98852_1000
libvorbis=1.3.7=h9c3ff4c_0
libwebp-base=1.2.4=h166bdaf_0
libxcb=1.13=h7f98852_1004
libxkbcommon=1.0.3=he3ba5ed_0
libxml2=2.10.3=h7463322_0
libzlib=1.2.13=h166bdaf_4
libzopfli=1.0.3=h9c3ff4c_0
link-traits=1.0.3=pyhd8ed1ab_3
locket=1.0.0=pyhd8ed1ab_0
lz4-c=1.9.3=h9c3ff4c_1
matplotlib-base=3.6.1=py310h8d5ebf3_1
matplotlib-inline=0.1.6=pyhd8ed1ab_0
mpc=1.2.1=h9f54685_0
mpfr=4.1.0=h9202a9a_1
mpg123=1.30.2=h27087fc_1
mpmath=1.2.1=pyhd8ed1ab_0
mrcz=0.5.6=pyh9f0ad1d_1
msgpack-python=1.0.4=py310hbf28c38_0
munkres=1.1.4=pyh9f0ad1d_0
mysql-common=8.0.31=haf5c9bc_0
mysql-libs=8.0.31=h28c427c_0
natsort=8.2.0=pyhd8ed1ab_0
nbformat=5.7.0=pyhd8ed1ab_0
ncurses=6.3=h27087fc_1
nest-asyncio=1.5.6=pyhd8ed1ab_0
networkx=2.8.7=pyhd8ed1ab_0
nomkl=1.0=h5ca1d4c_0
nspr=4.32=h9c3ff4c_1
nss=3.78=h2350873_0
openjpeg=2.5.0=h7d73246_1
openssl=1.1.1s=h166bdaf_0
packaging=21.3=pyhd8ed1ab_0
parso=0.8.3=pyhd8ed1ab_0
partd=1.3.0=pyhd8ed1ab_0
pcre2=10.37=hc3806b6_1
pexpect=4.8.0=pyh9f0ad1d_2
pickleshare=0.7.5=py_1003
pint=0.19.2=pyhd8ed1ab_0
pip=22.2.2=pyhd8ed1ab_0
pkgutil-resolve-name=1.3.10=pyhd8ed1ab_0
ply=3.11=py_1
prettytable=3.4.1=pyhd8ed1ab_0
prompt-toolkit=3.0.31=pyha770c72_0
pthread-stubs=0.4=h36c2ea0_1001
ptyprocess=0.7.0=pyhd3deb0d_0
pulseaudio=14.0=habe0971_10
pure_eval=0.2.2=pyhd8ed1ab_0
pycparser=2.21=pyhd8ed1ab_0
pyface=7.4.2=pyhd8ed1ab_0
pygments=2.13.0=pyhd8ed1ab_0
pyopenssl=22.0.0=pyhd8ed1ab_1
pyparsing=3.0.9=pyhd8ed1ab_0
pyqt=5.15.7=py310h29803b5_2
pysocks=1.7.1=pyha2e5f31_6
python=3.10.6=h582c2e5_0_cpython
python-blosc=1.10.6=py310h769672d_1
python-dateutil=2.8.2=pyhd8ed1ab_0
python-fastjsonschema=2.16.2=pyhd8ed1ab_0
python_abi=3.10=2_cp310
pytz=2022.6=pyhd8ed1ab_0
pyusid=0.0.10=pyhd8ed1ab_0
qt-main=5.15.6=hc525480_0
readline=8.1.2=h0f457ee_0
requests=2.28.1=pyhd8ed1ab_1
setuptools=65.4.0=pyhd8ed1ab_0
sidpy=0.11=pyhd8ed1ab_0
six=1.16.0=pyh6c4a22f_0
snappy=1.1.9=hbd366e4_1
sortedcontainers=2.4.0=pyhd8ed1ab_0
sparse=0.13.0=pyhd8ed1ab_0
sqlite=3.39.3=h5082296_0
stack_data=0.5.1=pyhd8ed1ab_0
tblib=1.7.0=pyhd8ed1ab_0
threadpoolctl=3.1.0=pyh8a188c0_0
tifffile=2022.8.12=pyhd8ed1ab_0
tk=8.6.12=h27826a3_0
toml=0.10.2=pyhd8ed1ab_0
toolz=0.12.0=pyhd8ed1ab_0
tqdm=4.64.1=pyhd8ed1ab_0
traitlets=5.4.0=pyhd8ed1ab_0
traitsui=7.4.1=pyhd8ed1ab_0
typing-extensions=4.3.0=hd8ed1ab_0
typing_extensions=4.3.0=pyha770c72_0
tzdata=2022d=h191b570_0
urllib3=1.26.11=pyhd8ed1ab_0
wcwidth=0.2.5=pyh9f0ad1d_2
wheel=0.37.1=pyhd8ed1ab_0
widgetsnbextension=4.0.3=pyhd8ed1ab_0
xcb-util=0.4.0=h166bdaf_0
xcb-util-image=0.4.0=h166bdaf_0
xcb-util-keysyms=0.4.0=h166bdaf_0
xcb-util-renderutil=0.3.9=h166bdaf_0
xcb-util-wm=0.4.1=h166bdaf_0
xorg-libxau=1.0.9=h7f98852_0
xorg-libxdmcp=1.1.3=h7f98852_0
xz=5.2.6=h166bdaf_0
yaml=0.2.5=h7f98852_2
zarr=2.13.2=pyhd8ed1ab_1
zeromq=4.3.4=h9c3ff4c_1
zfp=1.0.0=h27087fc_1
zict=2.2.0=pyhd8ed1ab_0
zipp=3.8.1=pyhd8ed1ab_0
zlib=1.2.13=h166bdaf_4
zlib-ng=2.0.6=h166bdaf_0
zstd=1.5.2=h6239696_4
pip:
prefix: /home/hbrown/anaconda3/envs/hyperspy
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