pycroscopy issueshttps://code.ornl.gov/rvv/pycroscopy/-/issues2020-05-12T02:09:55Zhttps://code.ornl.gov/rvv/pycroscopy/-/issues/219Image shifting and saving as new dset2020-05-12T02:09:55ZVasudevan, Rama K.Image shifting and saving as new dset*Created by: rajgiriUW*
This came up when trying to align some images, but I didn't see anything already that resaves the shifted data. It's very simple but maybe I can just append to the old notebook about registration on the site? Or ...*Created by: rajgiriUW*
This came up when trying to align some images, but I didn't see anything already that resaves the shifted data. It's very simple but maybe I can just append to the old notebook about registration on the site? Or some simple function that just:
a) shifts array by specified amount
b) visualize pre and post-shifting
c) create a results group ("Shifted")
d) write using the pos/spec of the original dataset.https://code.ornl.gov/rvv/pycroscopy/-/issues/206Separate translator(s) for DM3 and DM4 files2019-06-06T15:38:58ZVasudevan, Rama K.Separate translator(s) for DM3 and DM4 files*Created by: ssomnath*
Currently, DM3 and DM4 translation is being managed by the image, time series, movie, image stack translators. These translators were originally designed to read multiple file formats given the similarities in the...*Created by: ssomnath*
Currently, DM3 and DM4 translation is being managed by the image, time series, movie, image stack translators. These translators were originally designed to read multiple file formats given the similarities in the operations. However, it is not clear to the end user as to which translator to use given a DM3/4 file. Perhaps the common elements in these translators could be reused or moved into static functions outside a translator class so that they can be shared across translators.
This change will be very important when attempting to build a look-up table that automates the translation process based off file extensions or signatures within the header. Such a feature would be the foundation for both a high level "load()" function as well as the development of a pipeline that connects (offline) instruments to data facilities.https://code.ornl.gov/rvv/pycroscopy/-/issues/169Request for interactive visualization tool for Dataset results from Process C...2018-06-15T15:12:17ZVasudevan, Rama K.Request for interactive visualization tool for Dataset results from Process Class *Created by: nmosto*
I'm putting in a request for a interactive visualization tool for dataset results from the Process class.
What I was envisioning was a LHS interactive spatial map where you can specify a parameter to visualize (suc...*Created by: nmosto*
I'm putting in a request for a interactive visualization tool for dataset results from the Process class.
What I was envisioning was a LHS interactive spatial map where you can specify a parameter to visualize (such as max amplitude). The RHS would inherit all of the data associated with a chosen pixel from the LHS and one can do what they want with it like apply new functions or make new plots.
For example taking the LHS spatial map of a fitting parameter and the RHS could plot the fit using that parameter back over the raw data to check what happened.https://code.ornl.gov/rvv/pycroscopy/-/issues/168Implement a way to update existing data to new version requirements2018-06-11T16:26:57ZVasudevan, Rama K.Implement a way to update existing data to new version requirements*Created by: CompPhysChris*
We try to keep updates from breaking backwards compatibility, but some of our new requirements have resulted in results from previous versions no longer being valid. We need to implement a version check and ...*Created by: CompPhysChris*
We try to keep updates from breaking backwards compatibility, but some of our new requirements have resulted in results from previous versions no longer being valid. We need to implement a version check and automatic updating system to correct for any changes in the code.
These updates need to be tied to a specific version and will be applied sequentially from the version of the file to the current version.https://code.ornl.gov/rvv/pycroscopy/-/issues/167loop_fitter missing checks for existing results2018-06-11T15:21:41ZVasudevan, Rama K.loop_fitter missing checks for existing results*Created by: ramav87*
do_guess and do_fit methods from BELoopFitter are missing override options that have been added to SHOFitter. This causes an error in the latest BE processing notebook.*Created by: ramav87*
do_guess and do_fit methods from BELoopFitter are missing override options that have been added to SHOFitter. This causes an error in the latest BE processing notebook.https://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/139Add datatype information to PycroData output2018-04-19T12:27:04ZVasudevan, Rama K.Add datatype information to PycroData output*Created by: CompPhysChris*
Easy way to access the dtype info especially field names for compound types.*Created by: CompPhysChris*
Easy way to access the dtype info especially field names for compound types.https://code.ornl.gov/rvv/pycroscopy/-/issues/134upload con conda-forge2018-03-29T21:19:14ZVasudevan, Rama K.upload con conda-forge*Created by: carlodri*
I was wondering if you were interested in uploading the package on conda-forge, which, as you probably know, is a widespread and robust package managing system. If you agree, I can prepare the feedstock recipe.*Created by: carlodri*
I was wondering if you were interested in uploading the package on conda-forge, which, as you probably know, is a widespread and robust package managing system. If you agree, I can prepare the feedstock recipe.https://code.ornl.gov/rvv/pycroscopy/-/issues/106Generalized versions of interactive Jupyter data visualization UIs2018-04-28T23:23:15ZVasudevan, Rama K.Generalized versions of interactive Jupyter data visualization UIs*Created by: ssomnath*
Things from BEPS and image cleaning notebooks that would be useful for other applications should be generalized.*Created by: ssomnath*
Things from BEPS and image cleaning notebooks that would be useful for other applications should be generalized.https://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/98convert patch_be_lv_format to a translator2017-08-18T16:33:37ZVasudevan, Rama K.convert patch_be_lv_format to a translator*Created by: ssomnath*
*Created by: ssomnath*
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/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/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/43More elegant implementation of plot groups2016-12-14T18:54:42ZVasudevan, Rama K.More elegant implementation of plot groups*Created by: ssomnath*
Use region references instead of separate groups and datasets.*Created by: ssomnath*
Use region references instead of separate groups and datasets.https://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/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/36Ability to specify a list of components to reconstruct images with2016-12-14T16:15:10ZVasudevan, Rama K.Ability to specify a list of components to reconstruct images with*Created by: ssomnath*
in Image windowing*Created by: ssomnath*
in Image windowinghttps://code.ornl.gov/rvv/pycroscopy/-/issues/35Image windowing should accept ascii files as well2016-12-12T14:24:45ZVasudevan, Rama K.Image windowing should accept ascii files as well*Created by: ssomnath*
*Created by: ssomnath*
https://code.ornl.gov/rvv/pycroscopy/-/issues/31Port tree class2016-12-09T16:01:01ZVasudevan, Rama K.Port tree class*Created by: ssomnath*
Port the tree class from PySPM to pcroscopy
┆Issue is synchronized with this [Asana task](https://app.asana.com/0/200029249765524/202089936281820)
*Created by: ssomnath*
Port the tree class from PySPM to pcroscopy
┆Issue is synchronized with this [Asana task](https://app.asana.com/0/200029249765524/202089936281820)