pycroscopy issueshttps://code.ornl.gov/rvv/pycroscopy/-/issues2016-12-13T13:05:49Zhttps://code.ornl.gov/rvv/pycroscopy/-/issues/41BE noise floor should be a 2D dataset and should come with its own spectrosco...2016-12-13T13:05:49ZVasudevan, Rama K.BE noise floor should be a 2D dataset and should come with its own spectroscopic datasets*Created by: ssomnath*
*Created by: ssomnath*
https://code.ornl.gov/rvv/pycroscopy/-/issues/220BEOdfTranslator failure2020-05-15T19:44:20ZVasudevan, Rama K.BEOdfTranslator failure*Created by: ramav87*
BE ODF translator unable to translate certain old files collected in 2010. This error was found for nonlinearity measurements:
> ---------------------------------------------------------------------------
> K...*Created by: ramav87*
BE ODF translator unable to translate certain old files collected in 2010. This error was found for nonlinearity measurements:
> ---------------------------------------------------------------------------
> KeyError Traceback (most recent call last)
> <ipython-input-6-6c7fce848344> in <module>
> 4 translator = px.translators.BEodfTranslator()
> 5
> ----> 6 translator.translate(file_path)
>
> //anaconda3/lib/python3.7/site-packages/pycroscopy/io/translators/be_odf.py in translate(self, file_path, show_plots, save_plots, do_histogram, verbose)
> 251
> 252 if isBEPS:
> --> 253 (UDVS_labs, UDVS_units, UDVS_mat) = self.__build_udvs_table(parm_dict)
> 254
> 255 # Remove the unused plot group columns before proceeding:
>
> //anaconda3/lib/python3.7/site-packages/pycroscopy/io/translators/be_odf.py in __build_udvs_table(self, parm_dict)
> 1014 BE_amp = parm_dict['BE_amplitude_[V]']
> 1015
> -> 1016 VS_amp = parm_dict['VS_amplitude_[V]']
> 1017 VS_offset = parm_dict['VS_offset_[V]']
> 1018 # VS_read_voltage = parm_dict['VS_read_voltage_[V]']
>
> KeyError: 'VS_amplitude_[V]'
Will explore this in more detail.https://code.ornl.gov/rvv/pycroscopy/-/issues/25Better index tracking in the model class2016-12-06T19:19:56ZVasudevan, Rama K.Better index tracking in the model class*Created by: ssomnath*
When reading a large dataset in chunks, the get_data method updates the start and end indices by itself. This would cause serious problems when fitting since the indices would have moved to the next chunk even bef...*Created by: ssomnath*
When reading a large dataset in chunks, the get_data method updates the start and end indices by itself. This would cause serious problems when fitting since the indices would have moved to the next chunk even before the get_guess method can be called. Need a better book-keeping method to keep track of indices of the current chunk
┆Issue is synchronized with this [Asana task](https://app.asana.com/0/200029249765524/202083147009347)
https://code.ornl.gov/rvv/pycroscopy/-/issues/42Better naming conventions for units in attributes2016-12-13T13:07:31ZVasudevan, Rama K.Better naming conventions for units in attributes*Created by: ssomnath*
Currently attributes are named as "attribute_1_unit" for those with units and "attribute_2" for those without units. A parser looking for certain attributes would currently absorb "unit" and "2" as the units. We s...*Created by: ssomnath*
Currently attributes are named as "attribute_1_unit" for those with units and "attribute_2" for those without units. A parser looking for certain attributes would currently absorb "unit" and "2" as the units. We should be naming the attributes to something like "attribute_1__unit" or "attribute_1-unit" to avoid confusionhttps://code.ornl.gov/rvv/pycroscopy/-/issues/104dm3 translation in python 3 results in an Assertion Error2018-01-18T13:13:28ZVasudevan, Rama K.dm3 translation in python 3 results in an Assertion Error*Created by: ssomnath*
/io/translators/df_utils/parse_dm3.py in parse_dm_tag_data(f, outdata)
227 else:
228 _delim, header_len, data_type = get_from_file(f, "> 4s l l")
--> 229 assert(_delim == "%%%%")
...*Created by: ssomnath*
/io/translators/df_utils/parse_dm3.py in parse_dm_tag_data(f, outdata)
227 else:
228 _delim, header_len, data_type = get_from_file(f, "> 4s l l")
--> 229 assert(_delim == "%%%%")
230 ret, header = dm_types[data_type](f)
231 assert(header + 1 == header_len)https://code.ornl.gov/rvv/pycroscopy/-/issues/70Fix the dendrogram plotting function2018-01-19T17:12:56ZVasudevan, Rama K.Fix the dendrogram plotting function*Created by: ssomnath*
*Created by: ssomnath*
https://code.ornl.gov/rvv/pycroscopy/-/issues/192Out of date notebooks2018-10-08T16:58:27ZVasudevan, Rama K.Out of date notebooks*Created by: DancingQuanta*
I am trying to do a tutorial here Tutorial_04_Interactive_Visualization. But I found that some things are broken because the functions in the notebooks have been renamed, or changed functionality.
*Created by: DancingQuanta*
I am trying to do a tutorial here Tutorial_04_Interactive_Visualization. But I found that some things are broken because the functions in the notebooks have been renamed, or changed functionality.
https://code.ornl.gov/rvv/pycroscopy/-/issues/40Problem in automatically estimating window size in image windowing2016-12-14T16:06:56ZVasudevan, Rama K.Problem in automatically estimating window size in image windowing*Created by: ssomnath*
*Created by: ssomnath*
https://code.ornl.gov/rvv/pycroscopy/-/issues/157Reshape_to_n_dims for non-square images2018-05-26T21:22:05ZVasudevan, Rama K.Reshape_to_n_dims for non-square images*Created by: rajgiriUW*
Posted on Slack, but for tracking.
Issue is for non-square image files, I think the reshape_to_n_dims function is reordering the data when it shouldn't be, resulting in some jagged-looking images (if rows > co...*Created by: rajgiriUW*
Posted on Slack, but for tracking.
Issue is for non-square image files, I think the reshape_to_n_dims function is reordering the data when it shouldn't be, resulting in some jagged-looking images (if rows > columns) or the image is repeated vertically (if columns > rows).
Here's what happens when running this on an example:
Position dimensions: ['X' 'Y']
Position sort order: [0 1]
Spectroscopic Dimensions: ['arb']
Spectroscopic sort order: [0]
Position dimensions (sort applied): ['X' 'Y']
Position dimensionality (sort applied): [256, 128]
Spectroscopic dimensions (sort applied): ['arb']
Spectroscopic dimensionality (sort applied): [1]
After first reshape, labels are ['Y' 'X' 'arb']
Data shape is (128, 256, 1)
Axes will permuted in this order: [1 0 2]
New labels ordering: ['X' 'Y' 'arb']
Dataset now of shape: (256, 128, 1)
Suhas seems to think the issue is in line:
>> Axes will permuted in this order: [1 0 2]
Since that is changing the dimensions.
I confirmed in the Igor IBW Translator that the position dimensions are being written correctly. It is possible to correct the Translator to fix this, I think, but I then expect the issue to pop up in other translators.
https://code.ornl.gov/rvv/pycroscopy/-/issues/137sdist tarball has wrong contents2018-03-27T17:27:45ZVasudevan, Rama K.sdist tarball has wrong contents*Created by: carlodri*
the source tarball available on Pypi is not what it should be: it contains a number of nested directories but it doesn't have the structure of a package source. Is this deliberate?
This is strictly related to #...*Created by: carlodri*
the source tarball available on Pypi is not what it should be: it contains a number of nested directories but it doesn't have the structure of a package source. Is this deliberate?
This is strictly related to #134, since conda-forge is based on `sdist`tarballs.https://code.ornl.gov/rvv/pycroscopy/-/issues/239SVD error2020-12-20T20:58:51ZVasudevan, Rama K.SVD error*Created by: sulaymandesai*
Hi,
I have been following the example notebooks on this GitHub page to perform SVD. I get the following error:
```
1 decomposer = px.processing.svd_utils.SVD(h5_main, num_components=100)
----> 2 h5_s...*Created by: sulaymandesai*
Hi,
I have been following the example notebooks on this GitHub page to perform SVD. I get the following error:
```
1 decomposer = px.processing.svd_utils.SVD(h5_main, num_components=100)
----> 2 h5_svd_group = decomposer.compute()
3
4 h5_u = h5_svd_group['U']
5 h5_v = h5_svd_group['V']
~/.pyenv/versions/3.8.3/lib/python3.8/site-packages/pycroscopy/processing/svd_utils.py in compute(self, override)
161 """
162 if self.__u is None and self.__v is None and self.__s is None:
--> 163 self.test(override=override)
164
165 if self.h5_results_grp is None:
~/.pyenv/versions/3.8.3/lib/python3.8/site-packages/pycroscopy/processing/svd_utils.py in test(self, override)
137 raise ValueError('Could not reshape U to N-Dimensional dataset! Error:' + success)
138
--> 139 v_mat, success = reshape_to_n_dims(self.__v, h5_pos=np.expand_dims(np.arange(self.__u.shape[1]), axis=1),
140 h5_spec=self.h5_main.h5_spec_inds)
141 if not success:
~/.pyenv/versions/3.8.3/lib/python3.8/site-packages/pyUSID/io/hdf_utils/model.py in reshape_to_n_dims(h5_main, h5_pos, h5_spec, get_labels, verbose, sort_dims, lazy)
84 else:
85 if not isinstance(h5_main, (h5py.Dataset, np.ndarray, da.core.Array)):
---> 86 raise TypeError('h5_main should either be a h5py.Dataset or numpy array')
87
88 if h5_pos is not None:
TypeError: h5_main should either be a h5py.Dataset or numpy array
```
Any help would be appreciated!https://code.ornl.gov/rvv/pycroscopy/-/issues/152svd_rebuild error with get_component_slice returning ndarray2018-05-08T17:35:34ZVasudevan, Rama K.svd_rebuild error with get_component_slice returning ndarray*Created by: rajgiriUW*
in svd_utils.rebuild_svd:
comp_slice, num_comps = get_component_slice(components, total_components=h5_main.shape[1])
will cause an error later in:
n_comps = h5_S[comp_slice].size
if comp_slice is an ndarr...*Created by: rajgiriUW*
in svd_utils.rebuild_svd:
comp_slice, num_comps = get_component_slice(components, total_components=h5_main.shape[1])
will cause an error later in:
n_comps = h5_S[comp_slice].size
if comp_slice is an ndarray rather than a list. This seems to be an H5Py limitation.https://code.ornl.gov/rvv/pycroscopy/-/issues/156svd_utils.rebuild_svd bug in create_indexed_group2018-05-22T12:02:47ZVasudevan, Rama K.svd_utils.rebuild_svd bug in create_indexed_group*Created by: rajgiriUW*
I think this was a bug in commit f327da7d98907b9ba09473055320e12ddb04e122 in updating svd_utils:
line 328:
rebuilt_grp = create_indexed_group('Rebuilt_Data', h5_svd_group.name[1:])
throws an error sinc...*Created by: rajgiriUW*
I think this was a bug in commit f327da7d98907b9ba09473055320e12ddb04e122 in updating svd_utils:
line 328:
rebuilt_grp = create_indexed_group('Rebuilt_Data', h5_svd_group.name[1:])
throws an error since create_indexed_group requires a h5Py group, not string.
I think this change should work (will test):
rebuilt_grp = create_indexed_group(h5_svd_group, 'Rebuilt_Data')https://code.ornl.gov/rvv/pycroscopy/-/issues/64Window slices on mac are floats2018-01-18T13:10:48ZVasudevan, Rama K.Window slices on mac are floats*Created by: CompPhysChris*
The win_slices are all floats on Mac. Reported by Artem. uint+int is returning a float.*Created by: CompPhysChris*
The win_slices are all floats on Mac. Reported by Artem. uint+int is returning a float.