Adds entry point to create matplotlibrc parameters file #773
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Closes #761 Introduces the `topostats create-matplotlibrc` sub-command/entry point to write the default style file (`topostats/topostats.mplstyle`) to disk for modification and subsequent usage. The path and filename can be customised when invoking. This doesn't necessarily mean that all aspects of image plotting are controlled since we set default filenames, titles and DPI and whether an image is in the `core` set via the `topostats/plotting_dictionary.yaml` file. Documentation has been added that, hopefully, clarifies how to use this and points users users to the relevant Matplotlib documentation. Any further tweaking beyond the current state I feel pulls us towards writing a whole API for Matplotlib which is something that I am keen to avoid as users would be better served using the examples shown in the Notebook on [plotting scans](https://github.com/AFM-SPM/TopoStats/blob/main/notebooks/03-Plotting-scans.ipynb) to customise their plots to their own preferences.
ns-rse
requested review from
derollins,
SylviaWhittle,
MaxGamill-Sheffield and
llwiggins
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## main #773 +/- ##
==========================================
- Coverage 84.32% 84.30% -0.02%
==========================================
Files 21 21
Lines 3119 3128 +9
==========================================
+ Hits 2630 2637 +7
- Misses 489 491 +2 ☔ View full report in Codecov by Sentry. |
|
The This does allow important formatting changes to be made and it is good that all the various aspects of the images can be edited now. However from a broader usability perspective the key variables are hidden somewhat within a very large file, I had to try a few searches before I could find the right section to change the colour scale and the other setting I wanted to change, |
derollins
approved these changes
Jan 5, 2024
|
The generated file is, in terms of variable order, a carbon copy of the default Matplotlib from here a small number of fields have been changed. The DPI settings are handled on a per-image basis. I tried to describe how these are handled in the addition to the I'm disinclined to make a highly configurable plotting interface to TopoStats when one already exists in Matplotlib which is what the rc-file is doing. Images/graphs/figures have such a wide array of choices and tweaking them is in my view best done in a "Read-evaluate print loop" (REPL) manner in Jupyter Notebooks where instant feedback on the image is obtained. If multiple files need processing with the same parameters then once these have been determined they can be transferred to the configuration file and applied to a batch of images. |
ns-rse
added a commit
that referenced
this pull request
Jan 12, 2024
Closes #776 + Aligns command line and configuration field names with those in matplotlibrc files. + Restores the `cmap` configuration option to `default_config.yaml` and introduces `savefig_dpi` option. + Adds command line options for setting DPI (`--savefig-dpi`), Colormap (`--cmap`)and Output file format (`--savefig-format`). + Expands documentation on how to use custom configuration files or command line options to set the DPI/Colormap/Output format. + Updates the header to `topostats.mplstyle` to explain how to use it as typically users will have created a copy of the file (after the convenience function `topostats create-matplotlibrc` was introduced with #773). + To achieve this the dictionary `config["plotting"]` needed explicitly updating as the `update_config()` function doesn't update nested configurations (since this is the first PR that introduces command line options that modify any of the values in the nested dictionaries). + Updates options for `topostats toposum`` to align with `savefig_format` and adds flag to entry point so output format is consistent. + Updates and expands the configuration documentation explaining how to use these conveniences. As a consequence quite a few files are touched to ensure that validation and processing functions all have variables that align with those in the configuration. If users could test this it would be very much appreciated, if you use the Git installed version something like the following would switch branches and allow you test it. ``` conda create --name topostats-config # Create and activate a virtual env specific to this conda activate topostats-config cd ~/path/to/TopoStats git pull git checkout ns-rse/776-config-jigging pip install -e . topostats process --output-dir base topostats create-config test_config.yaml # Create test_config.yaml to try changing parameters topostats process --config test_config.yaml --output-dir test1 topostats process --output-dir test2 --savefig-dpi 10 --cmap rainbow --savefig-format svg topostats process --config test_config.yaml --output-dir test3 --savefig-dpi 80 --cmap viridis --savefig-format pdf ``` Each invocation of `topostats process` will save output to its own directory (either `base`, `test1`, `test2` and `test3`) for comparison. There should be differences between each `base` the values used in `test_config.yaml` and saved under `test1` and those under `test2` and `test3` should also differ. I would really appreciate feedback on the documentation as without clear documentation it is perhaps confusing how the components interact and work and can be modified and getting this as clear as possible will be really helpful.
ns-rse
added a commit
that referenced
this pull request
Jan 12, 2024
Closes #776 + Aligns command line and configuration field names with those in matplotlibrc files. + Restores the `cmap` configuration option to `default_config.yaml` and introduces `savefig_dpi` option. + Adds command line options for setting DPI (`--savefig-dpi`), Colormap (`--cmap`)and Output file format (`--savefig-format`). + Expands documentation on how to use custom configuration files or command line options to set the DPI/Colormap/Output format. + Updates the header to `topostats.mplstyle` to explain how to use it as typically users will have created a copy of the file (after the convenience function `topostats create-matplotlibrc` was introduced with #773). + To achieve this the dictionary `config["plotting"]` needed explicitly updating as the `update_config()` function doesn't update nested configurations (since this is the first PR that introduces command line options that modify any of the values in the nested dictionaries). + Updates options for `topostats toposum`` to align with `savefig_format` and adds flag to entry point so output format is consistent. + Updates and expands the configuration documentation explaining how to use these conveniences. As a consequence quite a few files are touched to ensure that validation and processing functions all have variables that align with those in the configuration. If users could test this it would be very much appreciated, if you use the Git installed version something like the following would switch branches and allow you test it. ``` conda create --name topostats-config # Create and activate a virtual env specific to this conda activate topostats-config cd ~/path/to/TopoStats git pull git checkout ns-rse/776-config-jigging pip install -e . topostats process --output-dir base topostats create-config test_config.yaml # Create test_config.yaml to try changing parameters topostats process --config test_config.yaml --output-dir test1 topostats process --output-dir test2 --savefig-dpi 10 --cmap rainbow --savefig-format svg topostats process --config test_config.yaml --output-dir test3 --savefig-dpi 80 --cmap viridis --savefig-format pdf ``` Each invocation of `topostats process` will save output to its own directory (either `base`, `test1`, `test2` and `test3`) for comparison. There should be differences between each `base` the values used in `test_config.yaml` and saved under `test1` and those under `test2` and `test3` should also differ. I would really appreciate feedback on the documentation as without clear documentation it is perhaps confusing how the components interact and work and can be modified and getting this as clear as possible will be really helpful.
ns-rse
added a commit
that referenced
this pull request
Jan 12, 2024
Closes #776 + Aligns command line and configuration field names with those in matplotlibrc files. + Restores the `cmap` configuration option to `default_config.yaml` and introduces `savefig_dpi` option. + Adds command line options for setting DPI (`--savefig-dpi`), Colormap (`--cmap`)and Output file format (`--savefig-format`). + Expands documentation on how to use custom configuration files or command line options to set the DPI/Colormap/Output format. + Updates the header to `topostats.mplstyle` to explain how to use it as typically users will have created a copy of the file (after the convenience function `topostats create-matplotlibrc` was introduced with #773). + To achieve this the dictionary `config["plotting"]` needed explicitly updating as the `update_config()` function doesn't update nested configurations (since this is the first PR that introduces command line options that modify any of the values in the nested dictionaries). + Updates options for `topostats toposum`` to align with `savefig_format` and adds flag to entry point so output format is consistent. + Updates and expands the configuration documentation explaining how to use these conveniences. As a consequence quite a few files are touched to ensure that validation and processing functions all have variables that align with those in the configuration. If users could test this it would be very much appreciated, if you use the Git installed version something like the following would switch branches and allow you test it. ``` conda create --name topostats-config # Create and activate a virtual env specific to this conda activate topostats-config cd ~/path/to/TopoStats git pull git checkout ns-rse/776-config-jigging pip install -e . topostats process --output-dir base topostats create-config test_config.yaml # Create test_config.yaml to try changing parameters topostats process --config test_config.yaml --output-dir test1 topostats process --output-dir test2 --savefig-dpi 10 --cmap rainbow --savefig-format svg topostats process --config test_config.yaml --output-dir test3 --savefig-dpi 80 --cmap viridis --savefig-format pdf ``` Each invocation of `topostats process` will save output to its own directory (either `base`, `test1`, `test2` and `test3`) for comparison. There should be differences between each `base` the values used in `test_config.yaml` and saved under `test1` and those under `test2` and `test3` should also differ. I would really appreciate feedback on the documentation as without clear documentation it is perhaps confusing how the components interact and work and can be modified and getting this as clear as possible will be really helpful.
ns-rse
added a commit
that referenced
this pull request
Jan 12, 2024
Closes #776 + Aligns command line and configuration field names with those in matplotlibrc files. + Restores the `cmap` configuration option to `default_config.yaml` and introduces `savefig_dpi` option. + Adds command line options for setting DPI (`--savefig-dpi`), Colormap (`--cmap`)and Output file format (`--savefig-format`). + Expands documentation on how to use custom configuration files or command line options to set the DPI/Colormap/Output format. + Updates the header to `topostats.mplstyle` to explain how to use it as typically users will have created a copy of the file (after the convenience function `topostats create-matplotlibrc` was introduced with #773). + To achieve this the dictionary `config["plotting"]` needed explicitly updating as the `update_config()` function doesn't update nested configurations (since this is the first PR that introduces command line options that modify any of the values in the nested dictionaries). + Updates options for `topostats toposum`` to align with `savefig_format` and adds flag to entry point so output format is consistent. + Updates and expands the configuration documentation explaining how to use these conveniences. As a consequence quite a few files are touched to ensure that validation and processing functions all have variables that align with those in the configuration. If users could test this it would be very much appreciated, if you use the Git installed version something like the following would switch branches and allow you test it. ``` conda create --name topostats-config # Create and activate a virtual env specific to this conda activate topostats-config cd ~/path/to/TopoStats git pull git checkout ns-rse/776-config-jigging pip install -e . topostats process --output-dir base topostats create-config test_config.yaml # Create test_config.yaml to try changing parameters topostats process --config test_config.yaml --output-dir test1 topostats process --output-dir test2 --savefig-dpi 10 --cmap rainbow --savefig-format svg topostats process --config test_config.yaml --output-dir test3 --savefig-dpi 80 --cmap viridis --savefig-format pdf ``` Each invocation of `topostats process` will save output to its own directory (either `base`, `test1`, `test2` and `test3`) for comparison. There should be differences between each `base` the values used in `test_config.yaml` and saved under `test1` and those under `test2` and `test3` should also differ. I would really appreciate feedback on the documentation as without clear documentation it is perhaps confusing how the components interact and work and can be modified and getting this as clear as possible will be really helpful.
ns-rse
added a commit
that referenced
this pull request
Jan 12, 2024
Closes #776 + Aligns command line and configuration field names with those in matplotlibrc files. + Restores the `cmap` configuration option to `default_config.yaml` and introduces `savefig_dpi` option. + Adds command line options for setting DPI (`--savefig-dpi`), Colormap (`--cmap`)and Output file format (`--savefig-format`). + Expands documentation on how to use custom configuration files or command line options to set the DPI/Colormap/Output format. + Updates the header to `topostats.mplstyle` to explain how to use it as typically users will have created a copy of the file (after the convenience function `topostats create-matplotlibrc` was introduced with #773). + To achieve this the dictionary `config["plotting"]` needed explicitly updating as the `update_config()` function doesn't update nested configurations (since this is the first PR that introduces command line options that modify any of the values in the nested dictionaries). + Updates options for `topostats toposum`` to align with `savefig_format` and adds flag to entry point so output format is consistent. + Updates and expands the configuration documentation explaining how to use these conveniences. As a consequence quite a few files are touched to ensure that validation and processing functions all have variables that align with those in the configuration. If users could test this it would be very much appreciated, if you use the Git installed version something like the following would switch branches and allow you test it. ``` conda create --name topostats-config # Create and activate a virtual env specific to this conda activate topostats-config cd ~/path/to/TopoStats git pull git checkout ns-rse/776-config-jigging pip install -e . topostats process --output-dir base topostats create-config test_config.yaml # Create test_config.yaml to try changing parameters topostats process --config test_config.yaml --output-dir test1 topostats process --output-dir test2 --savefig-dpi 10 --cmap rainbow --savefig-format svg topostats process --config test_config.yaml --output-dir test3 --savefig-dpi 80 --cmap viridis --savefig-format pdf ``` Each invocation of `topostats process` will save output to its own directory (either `base`, `test1`, `test2` and `test3`) for comparison. There should be differences between each `base` the values used in `test_config.yaml` and saved under `test1` and those under `test2` and `test3` should also differ. I would really appreciate feedback on the documentation as without clear documentation it is perhaps confusing how the components interact and work and can be modified and getting this as clear as possible will be really helpful.
ns-rse
added a commit
that referenced
this pull request
Feb 6, 2024
Closes #776 + Aligns command line and configuration field names with those in matplotlibrc files. + Restores the `cmap` configuration option to `default_config.yaml` and introduces `savefig_dpi` option. + Adds command line options for setting DPI (`--savefig-dpi`), Colormap (`--cmap`)and Output file format (`--savefig-format`). + Expands documentation on how to use custom configuration files or command line options to set the DPI/Colormap/Output format. + Updates the header to `topostats.mplstyle` to explain how to use it as typically users will have created a copy of the file (after the convenience function `topostats create-matplotlibrc` was introduced with #773). + To achieve this the dictionary `config["plotting"]` needed explicitly updating as the `update_config()` function doesn't update nested configurations (since this is the first PR that introduces command line options that modify any of the values in the nested dictionaries). + Updates options for `topostats toposum`` to align with `savefig_format` and adds flag to entry point so output format is consistent. + Updates and expands the configuration documentation explaining how to use these conveniences. As a consequence quite a few files are touched to ensure that validation and processing functions all have variables that align with those in the configuration. If users could test this it would be very much appreciated, if you use the Git installed version something like the following would switch branches and allow you test it. ``` conda create --name topostats-config # Create and activate a virtual env specific to this conda activate topostats-config cd ~/path/to/TopoStats git pull git checkout ns-rse/776-config-jigging pip install -e . topostats process --output-dir base topostats create-config test_config.yaml # Create test_config.yaml to try changing parameters topostats process --config test_config.yaml --output-dir test1 topostats process --output-dir test2 --savefig-dpi 10 --cmap rainbow --savefig-format svg topostats process --config test_config.yaml --output-dir test3 --savefig-dpi 80 --cmap viridis --savefig-format pdf ``` Each invocation of `topostats process` will save output to its own directory (either `base`, `test1`, `test2` and `test3`) for comparison. There should be differences between each `base` the values used in `test_config.yaml` and saved under `test1` and those under `test2` and `test3` should also differ. I would really appreciate feedback on the documentation as without clear documentation it is perhaps confusing how the components interact and work and can be modified and getting this as clear as possible will be really helpful.
ns-rse
added a commit
that referenced
this pull request
Feb 6, 2024
Closes #776 + Aligns command line and configuration field names with those in matplotlibrc files. + Restores the `cmap` configuration option to `default_config.yaml` and introduces `savefig_dpi` option. + Adds command line options for setting DPI (`--savefig-dpi`), Colormap (`--cmap`)and Output file format (`--savefig-format`). + Expands documentation on how to use custom configuration files or command line options to set the DPI/Colormap/Output format. + Updates the header to `topostats.mplstyle` to explain how to use it as typically users will have created a copy of the file (after the convenience function `topostats create-matplotlibrc` was introduced with #773). + To achieve this the dictionary `config["plotting"]` needed explicitly updating as the `update_config()` function doesn't update nested configurations (since this is the first PR that introduces command line options that modify any of the values in the nested dictionaries). + Updates options for `topostats toposum`` to align with `savefig_format` and adds flag to entry point so output format is consistent. + Updates and expands the configuration documentation explaining how to use these conveniences. As a consequence quite a few files are touched to ensure that validation and processing functions all have variables that align with those in the configuration. If users could test this it would be very much appreciated, if you use the Git installed version something like the following would switch branches and allow you test it. ``` conda create --name topostats-config # Create and activate a virtual env specific to this conda activate topostats-config cd ~/path/to/TopoStats git pull git checkout ns-rse/776-config-jigging pip install -e . topostats process --output-dir base topostats create-config test_config.yaml # Create test_config.yaml to try changing parameters topostats process --config test_config.yaml --output-dir test1 topostats process --output-dir test2 --savefig-dpi 10 --cmap rainbow --savefig-format svg topostats process --config test_config.yaml --output-dir test3 --savefig-dpi 80 --cmap viridis --savefig-format pdf ``` Each invocation of `topostats process` will save output to its own directory (either `base`, `test1`, `test2` and `test3`) for comparison. There should be differences between each `base` the values used in `test_config.yaml` and saved under `test1` and those under `test2` and `test3` should also differ. I would really appreciate feedback on the documentation as without clear documentation it is perhaps confusing how the components interact and work and can be modified and getting this as clear as possible will be really helpful.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Closes #761
Introduces the
topostats create-matplotlibrcsub-command/entry point to write the default style file (topostats/topostats.mplstyle) to disk for modification and subsequent usage. The path and filename can be customised when invoking.This doesn't necessarily mean that all aspects of image plotting are controlled since we set default filenames, titles and DPI and whether an image is in the
coreset via thetopostats/plotting_dictionary.yamlfile.Documentation has been added that, hopefully, clarifies how to use this in light of this and points users to the relevant Matplotlib documentation for customising parameters in the generated configuration file.
@derollins : I've included you as a reviewer as you requested this feature in #761. I've tested and it seems to work from my perspective in that I can create a sample configuration file of a given name in a given location but I would be very grateful if you could give it a whirl and provide feedback.
To do so you need to something similar to the following...
Once done you can remove the conda environment with...