brunorpinho / tsvi Goto Github PK

Here is a list of some packages not in the requirements that we may want to put in requirements-dev

• hvplot
• geoviews
• vega_datasets
• pydataset
• [ ]
  *N.B. for geoviews I had to first
  conda install --channel conda-forge cartopy
  to get around the error

GEOS version 3.6.2 is installed, but cartopy requires at least version 3.7.2.

See https://stackoverflow.com/questions/53697814/using-pip-install-to-install-cartopy-but-missing-proj-version-at-least-4-9-0 & https://github.com/SciTools/cartopy/issues/1239

Note book is running on a fresh pull. It shows me the files that are right here, but it would be nice to be able to navigate to a different data folder

While TSVI is intended to be quite general, the specific use case it will initially evolve around is mth5 magnetotelluric data archives.

Some mth5 data archives should be provided as files.

Here is a synthetic example from aurora. This should contain two stations, one called "test1" and the other called "test2"
test12rr.h5.gz

Here is a link to a 4-station archive being developed in the aurora cas04 tests.

@brunorpinho I want to add some branches to this repo. Can you add kkappler (https://github.com/kkappler) as a collaborator?

pyc files are showing as changes ... need to update .gitignore

There should be a data container "before plotting" that holds the data (and metadata) right before plot.

make_plot would then be factored into two methods:

1. A method that extracts the relevant data to plot from the xarray (or other) and stores it, applying operations such as demeaning (and perhaps filtering in future etc.)
2. A plot method that takes the formatted data container and serves the plots to the panel GUI

• Add x's in the corner of plot windows so they can be closed if not needed anymore
• Files tab not updating when new set of inputs from Folders tab is selected

@brunorpinho can you give Ian permission to push to the repo?
Do you need any info besides his github username (ThePattersonian)?

When using the CSV reader, after selecting a csv and plotting a graph, selecting new csvs do not show up in the selected Files dropdown list.

Just need a boilerplate yaml for now, and set up some placeholder tests

Pasted below is what I get in my notebook when I run the second cell.

It seems to be because of the call to
hv.opts(hv.opts.Rectangles(alpha = 0.5))

I commented out this line and committed

Traceback (most recent call last):
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/IPython/core/interactiveshell.py", line 3398, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "/tmp/ipykernel_24556/3055941099.py", line 10, in <cell line: 10>
hv.opts(hv.opts.Rectangles(alpha = 0.5))
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/param/parameterized.py", line 3654, in new
return inst.call(*args,**params)
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/holoviews/util/init.py", line 110, in call
self._linemagic(args[0])
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/holoviews/util/init.py", line 277, in _linemagic
options, failure = cls._process_magic(options, strict, backends=backends)
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/holoviews/util/init.py", line 255, in _process_magic
errmsg = StoreOptions.validation_error_message(options, backends=backends)
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/holoviews/core/options.py", line 1597, in validation_error_message
cls.validate_spec(spec, backends=backends)
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/holoviews/core/options.py", line 1571, in validate_spec
cls.apply_customizations(spec, options)
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/holoviews/core/options.py", line 1546, in apply_customizations
customization = {k:v.keywords_target(key.split('.')[0])
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/holoviews/core/options.py", line 1546, in
customization = {k:v.keywords_target(key.split('.')[0])
AttributeError: 'float' object has no attribute 'keywords_target'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/IPython/core/interactiveshell.py", line 1993, in showtraceback stb = self.InteractiveTB.structured_traceback(
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/IPython/core/ultratb.py", line 1118, in structured_traceback
return FormattedTB.structured_traceback(
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/IPython/core/ultratb.py", line 1012, in structured_traceback
return VerboseTB.structured_traceback(
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/IPython/core/ultratb.py", line 865, in structured_traceback
formatted_exception = self.format_exception_as_a_whole(etype, evalue, etb, number_of_lines_of_context,
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/IPython/core/ultratb.py", line 818, in format_exception_as_a_whole
frames.append(self.format_record(r))
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/IPython/core/ultratb.py", line 736, in format_record
result += ''.join(_format_traceback_lines(frame_info.lines, Colors, self.has_colors, lvals))
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/stack_data/utils.py", line 145, in cached_property_wrapper
value = obj.dict[self.func.name] = self.func(obj)
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/stack_data/core.py", line 698, in lines
pieces = self.included_pieces
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/stack_data/utils.py", line 145, in cached_property_wrapper
value = obj.dict[self.func.name] = self.func(obj)
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/stack_data/core.py", line 645, in included_pieces
scope_pieces = self.scope_pieces
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/stack_data/utils.py", line 145, in cached_property_wrapper
value = obj.dict[self.func.name] = self.func(obj)
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/stack_data/core.py", line 585, in scope_pieces
for piece in self.source.pieces
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/stack_data/utils.py", line 145, in cached_property_wrapper
value = obj.dict[self.func.name] = self.func(obj)
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/stack_data/core.py", line 90, in pieces
return list(self._clean_pieces())
File "/home/kkappler/anaconda2/envs/tsvi/lib/python3.9/site-packages/stack_data/core.py", line 114, in _clean_pieces
raise AssertionError("Pieces mismatches: %s" % mismatches)
AssertionError: Pieces mismatches: [{680, 681}, {696, 695}, {708, 709}, {714, 715}]

Need a flow of tests to run to look for and trace errors reproducibly

• Add datashader to setup.py if needed or use hvplot style import
• Make served panel application fill the browser window in

One solution would be:

• Grey out the DataShade checkbox when matplotlib radiobutton is selected
• Force Datashade boolean to be ignored in the plotting function when matplotlib radiobutton selected

@ThePattersonian can you add your new setup file to a branch based on this issue?

This issue is about making a simple pre-prototype plotter that just shows five channels from an mth5 file which we can use as an example to embed into the UI.

This can be done with matplotlib, but we later will use the newer tools like panel, holoviews, datashader etc.