pycroscopy issueshttps://code.ornl.gov/rvv/pycroscopy/-/issues2018-04-17T18:43:53Zhttps://code.ornl.gov/rvv/pycroscopy/-/issues/140be_viz_utils.jupyter_visualize_beps_sho not working for relaxation SHO fits2018-04-17T18:43:53ZVasudevan, Rama K.be_viz_utils.jupyter_visualize_beps_sho not working for relaxation SHO fits*Created by: ramav87*
Need to check dimensional reshaping
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-36-a0...*Created by: ramav87*
Need to check dimensional reshaping
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-36-a04eb0cf2113> in <module>()
1 step_chan = 'DC_Offset'
----> 2 px.be_viz_utils.jupyter_visualize_beps_sho(h5_sho_fit, step_chan)
~\Documents\GitHub\pycroscopy\pycroscopy\viz\be_viz_utils.py in jupyter_visualize_beps_sho(pc_sho_dset, step_chan, resp_func, resp_label, cmap)
324 bias_slider = ax_bias.axvline(x=step_ind, color='r')
325
--> 326 img_map, img_cmap = plot_map(ax_map, spatial_map.T, show_xy_ticks=None)
327
328 map_title = '{} - {}={}'.format(sho_quantity, step_chan, bias_mat[step_ind][0])
~\Documents\GitHub\pycroscopy\pycroscopy\viz\plot_utils.py in plot_map(axis, img, show_xy_ticks, show_cbar, x_size, y_size, num_ticks, stdevs, cbar_label, tick_font_size, origin, **kwargs)
430 kwargs.update({'origin': origin})
431
--> 432 im_handle = axis.imshow(img, **kwargs)
433
434 if show_xy_ticks is True:
~\AppData\Local\Continuum\anaconda3\lib\site-packages\matplotlib\__init__.py in inner(ax, *args, **kwargs)
1843 "the Matplotlib list!)" % (label_namer, func.__name__),
1844 RuntimeWarning, stacklevel=2)
-> 1845 return func(ax, *args, **kwargs)
1846
1847 inner.__doc__ = _add_data_doc(inner.__doc__,
~\AppData\Local\Continuum\anaconda3\lib\site-packages\matplotlib\axes\_axes.py in imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, **kwargs)
5471 resample=resample, **kwargs)
5472
-> 5473 im.set_data(X)
5474 im.set_alpha(alpha)
5475 if im.get_clip_path() is None:
~\AppData\Local\Continuum\anaconda3\lib\site-packages\matplotlib\image.py in set_data(self, A)
651 if not (self._A.ndim == 2
652 or self._A.ndim == 3 and self._A.shape[-1] in [3, 4]):
--> 653 raise TypeError("Invalid dimensions for image data")
654
655 if self._A.ndim == 3:
TypeError: Invalid dimensions for image datahttps://code.ornl.gov/rvv/pycroscopy/-/issues/1413+ Position support for loop visualizers2018-04-19T12:24:49ZVasudevan, Rama K.3+ Position support for loop visualizers*Created by: CompPhysChris*
The visualizers for the raw and SHO BE data have been updated to support more than 2 position dimensions. Similar updates need to be done to the loop visualizers.*Created by: CompPhysChris*
The visualizers for the raw and SHO BE data have been updated to support more than 2 position dimensions. Similar updates need to be done to the loop visualizers.https://code.ornl.gov/rvv/pycroscopy/-/issues/136BESHOFitter does not find existing results2018-05-22T19:11:31ZVasudevan, Rama K.BESHOFitter does not find existing results*Created by: CompPhysChris*
The Fitter method _check_for_old_guess does not find completed fits.*Created by: CompPhysChris*
The Fitter method _check_for_old_guess does not find completed fits.https://code.ornl.gov/rvv/pycroscopy/-/issues/135Plot attributes are hard coded2018-05-26T21:22:55ZVasudevan, Rama K.Plot attributes are hard coded*Created by: CompPhysChris*
Some plot attributes are being hard coded rather than pulled from the datasets. Ex: Field names in visualize_sho_results.*Created by: CompPhysChris*
Some plot attributes are being hard coded rather than pulled from the datasets. Ex: Field names in visualize_sho_results.https://code.ornl.gov/rvv/pycroscopy/-/issues/120BE processing Notebook2017-09-11T20:06:37ZVasudevan, Rama K.BE processing Notebook*Created by: ramav87*
Need ability to view the spatial maps of the Loop Fit parameters (V+, V-, Work of switching, etc.). Currently only allows visualization of the parameters of the loop fit function (a1,a2,b1,b2, etc.).*Created by: ramav87*
Need ability to view the spatial maps of the Loop Fit parameters (V+, V-, Work of switching, etc.). Currently only allows visualization of the parameters of the loop fit function (a1,a2,b1,b2, etc.).https://code.ornl.gov/rvv/pycroscopy/-/issues/119BE Processing Notebook2017-09-01T14:42:32ZVasudevan, Rama K.BE Processing Notebook*Created by: ramav87*
Colorbars needed for visualization of spatial maps, as well as export ("Save Figure") button for each visualizer.*Created by: ramav87*
Colorbars needed for visualization of spatial maps, as well as export ("Save Figure") button for each visualizer.https://code.ornl.gov/rvv/pycroscopy/-/issues/113Colorbar in BE processing notebook2017-08-09T14:15:48ZVasudevan, Rama K.Colorbar in BE processing notebook*Created by: ramav87*
All image plots need colorbars with units. Consistency across notebooks for this is also something we should work on. *Created by: ramav87*
All image plots need colorbars with units. Consistency across notebooks for this is also something we should work on. https://code.ornl.gov/rvv/pycroscopy/-/issues/105Igor ibw translation errors in python 32018-03-12T16:11:13ZVasudevan, Rama K.Igor ibw translation errors in python 3*Created by: ssomnath*
pycroscopy\io\translators\igor_ibw.py in _read_parms(ibw_wave)
173 Dictionary containing parameters
174 """
--> 175 parm_string = ibw_wave.get('note').decode('utf-8')
17...*Created by: ssomnath*
pycroscopy\io\translators\igor_ibw.py in _read_parms(ibw_wave)
173 Dictionary containing parameters
174 """
--> 175 parm_string = ibw_wave.get('note').decode('utf-8')
176 parm_string = parm_string.rstrip('\r')
177 parm_list = parm_string.split('\r')
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb0 in position 2200: invalid start bytehttps://code.ornl.gov/rvv/pycroscopy/-/issues/103MPI implementations for analysis and processing packages2017-07-18T13:18:23ZVasudevan, Rama K.MPI implementations for analysis and processing packages*Created by: ssomnath*
The idea is to provide an alternate framework for code to scale to multi CPU systems. The same scientific analysis and processing functions should be usable in the current multiprocessing implementation and the fu...*Created by: ssomnath*
The idea is to provide an alternate framework for code to scale to multi CPU systems. The same scientific analysis and processing functions should be usable in the current multiprocessing implementation and the future MPI implementations. This should ensure that scientists can continue to write / test / execute simple functions and minimal effort needs to be applied to scale the computation to a large number of cores / CPUshttps://code.ornl.gov/rvv/pycroscopy/-/issues/102Incorrect reshaping on loop projection2018-01-18T13:19:26ZVasudevan, Rama K.Incorrect reshaping on loop projection*Created by: ramav87*
Error in projectLoop batch (in be_loop_model) where order of reshaped array after loop projection is reversed from what it should be. *Created by: ramav87*
Error in projectLoop batch (in be_loop_model) where order of reshaped array after loop projection is reversed from what it should be. https://code.ornl.gov/rvv/pycroscopy/-/issues/101Ensure model classes accept a max_mem input2017-07-14T13:40:40ZVasudevan, Rama K.Ensure model classes accept a max_mem input*Created by: CompPhysChris*
The BE_SHO_model does not. Other models should be checked as well.
*Created by: CompPhysChris*
The BE_SHO_model does not. Other models should be checked as well.
https://code.ornl.gov/rvv/pycroscopy/-/issues/92Better version attributes in files2017-05-24T20:36:04ZVasudevan, Rama K.Better version attributes in files*Created by: ssomnath*
Add pycroscopy and underlying package (eg - scipy) versions to the datasets for any operation. These should be added to datasets and not datagroups to encompass the situation such as the Guess operation coming fro...*Created by: ssomnath*
Add pycroscopy and underlying package (eg - scipy) versions to the datasets for any operation. These should be added to datasets and not datagroups to encompass the situation such as the Guess operation coming from a different source (eg. instrumentation software) and the fit coming either from pycroscopy or BEAM etc.https://code.ornl.gov/rvv/pycroscopy/-/issues/82Improve analysis documentation.2017-04-11T12:29:44ZVasudevan, Rama K.Improve analysis documentation.*Created by: CompPhysChris*
*Created by: CompPhysChris*
https://code.ornl.gov/rvv/pycroscopy/-/issues/71Explore multi-core / faster alternatives to Kmeans and SVD2017-03-17T16:56:31ZVasudevan, Rama K.Explore multi-core / faster alternatives to Kmeans and SVD*Created by: ssomnath*
Look at arguments for Kmeans such as n_jobs and init to speed up K-means
We may need to look for anther package that speeds up SVD. *Created by: ssomnath*
Look at arguments for Kmeans such as n_jobs and init to speed up K-means
We may need to look for anther package that speeds up SVD. https://code.ornl.gov/rvv/pycroscopy/-/issues/47BEPS NDF translator needs to select N random spectra for Q factor checking2016-12-15T16:15:37ZVasudevan, Rama K.BEPS NDF translator needs to select N random spectra for Q factor checking*Created by: ssomnath*
This is necessary to figure out if we need to take the complex conjugate on the data*Created by: ssomnath*
This is necessary to figure out if we need to take the complex conjugate on the datahttps://code.ornl.gov/rvv/pycroscopy/-/issues/46Add the information criterion for SHO fits as well2016-12-14T19:43:33ZVasudevan, Rama K.Add the information criterion for SHO fits as well*Created by: ssomnath*
AIC / BIC*Created by: ssomnath*
AIC / BIChttps://code.ornl.gov/rvv/pycroscopy/-/issues/49repack in ioHDF5 still crashing2016-12-14T16:06:08ZVasudevan, Rama K.repack in ioHDF5 still crashing*Created by: ssomnath*
*Created by: ssomnath*
https://code.ornl.gov/rvv/pycroscopy/-/issues/38Ability to tell a (obviously) noisy image from a relatively clear image using...2016-12-09T19:45:12ZVasudevan, Rama K.Ability to tell a (obviously) noisy image from a relatively clear image using radially averaged correlation function*Created by: ssomnath*
*Created by: ssomnath*
https://code.ornl.gov/rvv/pycroscopy/-/issues/20Units and labels for data2016-12-14T14:44:50ZVasudevan, Rama K.Units and labels for data*Created by: ssomnath*
All main datasets should have appropriate labels and units attributes to tell visualizers / plotters about the data.
This applies to all translators.
The processing and analysis classes should either take copy th...*Created by: ssomnath*
All main datasets should have appropriate labels and units attributes to tell visualizers / plotters about the data.
This applies to all translators.
The processing and analysis classes should either take copy these attributes from the source dataset or create new attributes as appropriate
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