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@@ -0,0 +1 @@ +/FrozenPy-0.3.3.tar.gz diff --git a/python-frozenpy.spec b/python-frozenpy.spec new file mode 100644 index 0000000..7e63bf5 --- /dev/null +++ b/python-frozenpy.spec @@ -0,0 +1,254 @@ +%global _empty_manifest_terminate_build 0 +Name: python-FrozenPy +Version: 0.3.3 +Release: 1 +Summary: A small suit of function for analyzing freezing behavior based on a threshold. +License: MIT License +URL: https://github.com/MicTott/FrozenPy +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/4c/36/bb874c163e67bb2cdc373237115fb406673bdaa6c682905df50197850853/FrozenPy-0.3.3.tar.gz +BuildArch: noarch + +Requires: python3-numpy +Requires: python3-pandas + +%description +# FrozenPy + +FrozenPy is a small collection of Python functions for detecting freezing behavior and averaging data based on a threshold and experimental parameters, with a particular focus on Pavlovian conditioning paradigms. Freezing is detected by thresholding motion data under a defined value (e.g., 10 a.u.) for a defined minimum length of time (1 sec). It also includes functions for converting .out files generated from MedPC to easier-to-handle .csv files. + +FrozenPy is designed so that it is easy to add metadata (group, sex, etc.) and formats data for use with popular plotting (Seaborn) and statistical (Pingouin) packages within Python. + +## Usage + +#### Installation + +FrozenPy can easily be installed via [pip](https://pip.pypa.io/en/stable/installing/). Type the following into your terminal to install FrozenPy. + +```Python +pip install FrozenPy +``` + +#### Read .out files +Converting .out to .raw.csv, read .raw.csv: +```Python +# Base directory containing .out files +out_dir = '/path/to/your/.out/files' + +# convert all .out files within dir to .raw.csv +fp.read_out(out_dir) + +# read .raw.csv +data_raw = fp.read_rawcsv('your_data.raw.csv') +``` + +#### Detect freezing and average +Detect freezing: +```Python +# detect freezing +data_freezing = fp.detect_freezing(data_raw) +``` +This is an example for if we wanted to slice and average data with a 3 min baseline, 10s CS, 2s US, 58s ISI, and 5 trials: +```Python +# slice data +frz_bl, frz_trials = fp.get_averagedslices(df=data_freezing, + BL=180, + CS=10, + US=2, + Trials=5, + ISI=58, + fs=5, + Behav='Freezing') +``` + +This would output two variables: ```frz_bl``` which contained the averaged BL data for each subject, and ```frz_trials``` which contained CS, US, and ISI data for each subject. These are separated because BL is factorial data whereas Trials are repeated measures. + +## Notes + +This code was developed specifically for the [Maren Lab](http://marenlab.org/ "Maren Lab homepage") which uses MedPC boxes that measure motion via loadcells, but it should work with any motion data so long as it is in the correct format. If you notice any problems or wish to contribute please don't hesitate to contact me at mictott@gmail.com, open a pull request, or submit an issue. + +## Future directions + +* take advantage of xarrays (not in the near future) +* provide visible feedback to allow for threshold adjustments (not in the near future unless needed) + + + + +%package -n python3-FrozenPy +Summary: A small suit of function for analyzing freezing behavior based on a threshold. +Provides: python-FrozenPy +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-FrozenPy +# FrozenPy + +FrozenPy is a small collection of Python functions for detecting freezing behavior and averaging data based on a threshold and experimental parameters, with a particular focus on Pavlovian conditioning paradigms. Freezing is detected by thresholding motion data under a defined value (e.g., 10 a.u.) for a defined minimum length of time (1 sec). It also includes functions for converting .out files generated from MedPC to easier-to-handle .csv files. + +FrozenPy is designed so that it is easy to add metadata (group, sex, etc.) and formats data for use with popular plotting (Seaborn) and statistical (Pingouin) packages within Python. + +## Usage + +#### Installation + +FrozenPy can easily be installed via [pip](https://pip.pypa.io/en/stable/installing/). Type the following into your terminal to install FrozenPy. + +```Python +pip install FrozenPy +``` + +#### Read .out files +Converting .out to .raw.csv, read .raw.csv: +```Python +# Base directory containing .out files +out_dir = '/path/to/your/.out/files' + +# convert all .out files within dir to .raw.csv +fp.read_out(out_dir) + +# read .raw.csv +data_raw = fp.read_rawcsv('your_data.raw.csv') +``` + +#### Detect freezing and average +Detect freezing: +```Python +# detect freezing +data_freezing = fp.detect_freezing(data_raw) +``` +This is an example for if we wanted to slice and average data with a 3 min baseline, 10s CS, 2s US, 58s ISI, and 5 trials: +```Python +# slice data +frz_bl, frz_trials = fp.get_averagedslices(df=data_freezing, + BL=180, + CS=10, + US=2, + Trials=5, + ISI=58, + fs=5, + Behav='Freezing') +``` + +This would output two variables: ```frz_bl``` which contained the averaged BL data for each subject, and ```frz_trials``` which contained CS, US, and ISI data for each subject. These are separated because BL is factorial data whereas Trials are repeated measures. + +## Notes + +This code was developed specifically for the [Maren Lab](http://marenlab.org/ "Maren Lab homepage") which uses MedPC boxes that measure motion via loadcells, but it should work with any motion data so long as it is in the correct format. If you notice any problems or wish to contribute please don't hesitate to contact me at mictott@gmail.com, open a pull request, or submit an issue. + +## Future directions + +* take advantage of xarrays (not in the near future) +* provide visible feedback to allow for threshold adjustments (not in the near future unless needed) + + + + +%package help +Summary: Development documents and examples for FrozenPy +Provides: python3-FrozenPy-doc +%description help +# FrozenPy + +FrozenPy is a small collection of Python functions for detecting freezing behavior and averaging data based on a threshold and experimental parameters, with a particular focus on Pavlovian conditioning paradigms. Freezing is detected by thresholding motion data under a defined value (e.g., 10 a.u.) for a defined minimum length of time (1 sec). It also includes functions for converting .out files generated from MedPC to easier-to-handle .csv files. + +FrozenPy is designed so that it is easy to add metadata (group, sex, etc.) and formats data for use with popular plotting (Seaborn) and statistical (Pingouin) packages within Python. + +## Usage + +#### Installation + +FrozenPy can easily be installed via [pip](https://pip.pypa.io/en/stable/installing/). Type the following into your terminal to install FrozenPy. + +```Python +pip install FrozenPy +``` + +#### Read .out files +Converting .out to .raw.csv, read .raw.csv: +```Python +# Base directory containing .out files +out_dir = '/path/to/your/.out/files' + +# convert all .out files within dir to .raw.csv +fp.read_out(out_dir) + +# read .raw.csv +data_raw = fp.read_rawcsv('your_data.raw.csv') +``` + +#### Detect freezing and average +Detect freezing: +```Python +# detect freezing +data_freezing = fp.detect_freezing(data_raw) +``` +This is an example for if we wanted to slice and average data with a 3 min baseline, 10s CS, 2s US, 58s ISI, and 5 trials: +```Python +# slice data +frz_bl, frz_trials = fp.get_averagedslices(df=data_freezing, + BL=180, + CS=10, + US=2, + Trials=5, + ISI=58, + fs=5, + Behav='Freezing') +``` + +This would output two variables: ```frz_bl``` which contained the averaged BL data for each subject, and ```frz_trials``` which contained CS, US, and ISI data for each subject. These are separated because BL is factorial data whereas Trials are repeated measures. + +## Notes + +This code was developed specifically for the [Maren Lab](http://marenlab.org/ "Maren Lab homepage") which uses MedPC boxes that measure motion via loadcells, but it should work with any motion data so long as it is in the correct format. If you notice any problems or wish to contribute please don't hesitate to contact me at mictott@gmail.com, open a pull request, or submit an issue. + +## Future directions + +* take advantage of xarrays (not in the near future) +* provide visible feedback to allow for threshold adjustments (not in the near future unless needed) + + + + +%prep +%autosetup -n FrozenPy-0.3.3 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-FrozenPy -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 29 2023 Python_Bot <Python_Bot@openeuler.org> - 0.3.3-1 +- Package Spec generated @@ -0,0 +1 @@ +15b8888f33694074bff3be7dfa7c0c2b FrozenPy-0.3.3.tar.gz |