KiMoPack

https://kimopack.readthedocs.io/en/latest/
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KiMoPack is a Python library for loading, shaping, plotting, and fitting time-resolved spectral...
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### Install with user permissions

Source: https://kimopack.readthedocs.io/en/latest/_sources/Installation.rst.txt

Use the --user flag if the installation fails due to insufficient system rights.

```text
$ conda create --name kimoPack
	$ conda activate kimokack
	$ pip install KiMoPack h5py tables keyboard nbopen python-pptx --user
```

--------------------------------

### Install with user permissions

Source: https://kimopack.readthedocs.io/en/latest/Installation.html

Use this command if standard installation fails due to insufficient system rights.

```bash
$ conda create --name kimoPack
$ conda activate kimokack
$ pip install KiMoPack h5py tables keyboard nbopen python-pptx --user
```

--------------------------------

### Install KiMoPack with recommended dependencies

Source: https://kimopack.readthedocs.io/en/latest/_sources/Installation.rst.txt

Installs KiMoPack along with optional packages for file handling, presentation export, and notebook integration.

```text
$ pip install KiMoPack h5py tables nbopen python-pptx 
	(windows) python -m nbopen.install_win
	(Linux) python3 -m nbopen.install_xdg
	(MacOS) Clone the repository and run ./osx-install.sh
```

--------------------------------

### Install KiMoPack via pip

Source: https://kimopack.readthedocs.io/en/latest/Installation.html

Standard installation command using the pip package manager.

```bash
$ pip install KiMoPack
```

--------------------------------

### Install KiMoPack with recommended dependencies

Source: https://kimopack.readthedocs.io/en/latest/Installation.html

Installs KiMoPack along with optional packages for file handling, presentation export, and keyboard interrupts.

```bash
$ pip install KiMoPack h5py tables nbopen python-pptx
```

--------------------------------

### Install KiMoPack via conda

Source: https://kimopack.readthedocs.io/en/latest/Installation.html

Installation command using the conda package manager from the erdzeichen channel.

```bash
$ conda install -c erdzeichen kimopack
```

--------------------------------

### Create and configure a local conda environment

Source: https://kimopack.readthedocs.io/en/latest/Installation.html

Sets up a dedicated environment and installs KiMoPack with all recommended dependencies.

```bash
$ conda create --name kimoPack
$ conda activate kimokack
$ pip install KiMoPack h5py tables keyboard nbopen python-pptx
```

--------------------------------

### Initialize lmfit Parameters

Source: https://kimopack.readthedocs.io/en/latest/_sources/Fitting.rst.txt

The starting point for defining parameters for a fit.

```python
ta.par=lmfit.Parameters()
```

--------------------------------

### Upgrade KiMoPack

Source: https://kimopack.readthedocs.io/en/latest/Installation.html

Updates an existing installation to the latest version.

```bash
$ pip install KiMoPack -U
```

--------------------------------

### Install pytables via conda-forge

Source: https://kimopack.readthedocs.io/en/latest/Installation.html

Resolves potential issues with pytables by using the conda-forge distribution.

```bash
conda install -c conda-forge pytables
```

--------------------------------

### Download KiMoPack resources

Source: https://kimopack.readthedocs.io/en/latest/_sources/Installation.rst.txt

Use these commands in a Python console to fetch either the full set of notebooks and tutorials or only the workflow tools.

```python
import KiMoPack; KiMoPack.download_all()
```

```python
import KiMoPack; KiMoPack.download_notebooks()
```

--------------------------------

### Download KiMoPack notebooks via command line

Source: https://kimopack.readthedocs.io/en/latest/Installation.html

Use these one-liners to download workflow tools into your current directory.

```bash
ipython -c "import KiMoPack; KiMoPack.download_notebooks()"
python -c "import KiMoPack; KiMoPack.download_notebooks()"
python3 -c "import KiMoPack; KiMoPack.download_notebooks()"
```

--------------------------------

### Create a conda environment with specific Python version

Source: https://kimopack.readthedocs.io/en/latest/Installation.html

Sets up an environment with a specific Python version and Jupyter tools.

```bash
$ conda create --name kimopack python=3.11 ipython jupyterlab jupyter
$ conda activate kimopack
$ pip install KiMoPack h5py tables keyboard nbopen python-pptx
```

--------------------------------

### Save Project as HDF5

Source: https://kimopack.readthedocs.io/en/latest/Saving.html

Serializes the project state, including parameters, fit results, and raw data, into an HDF5 file. External fit functions must be re-assigned after reloading.

```python
self.Save_project()
```

--------------------------------

### Global fitting with multiple files

Source: https://kimopack.readthedocs.io/en/latest/_sources/Fitting.rst.txt

Perform global fitting across multiple projects using a unique parameter to differentiate models.

```python
ta.Fit_Global(multi_project = ta_list, unique_parameter = 'pump_power')
ta.Fit_Global(multi_project = ta_list, unique_parameter = 'pump_power', weights = [1/power1,1/power2])
```

--------------------------------

### self.Compare_at_wave()

Source: https://kimopack.readthedocs.io/en/latest/Comparing.html

Plots multiple kinetics into the same figure at one or multiple given wavelengths, supporting normalization and scaling.

```APIDOC
## self.Compare_at_wave()

### Description
Plots multiple kinetics into the same figure at one or multiple given wavelengths (rel_wave). It allows for normalization and scaling, with the spectral window width defined by the width parameter or ta.wavelength_bin.

### Usage
Useful for comparing kinetics across different quencher concentrations, pump powers, or fits.
```

--------------------------------

### Download workflow notebooks

Source: https://kimopack.readthedocs.io/en/latest/_sources/Installation.rst.txt

One-line commands to download the provided Jupyter notebook workflows.

```text
ipython -c "import KiMoPack; KiMoPack.download_notebooks()"
	python -c "import KiMoPack; KiMoPack.download_notebooks()"
	python3 -c "import KiMoPack; KiMoPack.download_notebooks()"
```

--------------------------------

### Manual DAS Calculation for same_DAS=False

Source: https://kimopack.readthedocs.io/en/latest/Fitting.html

Iterate through a list of projects to manually update parameters and perform global fitting when shared DAS is disabled.

```python
for ta_local in projects_list:
        local_fitted_parameter=ta.par_fit
        try:
                for key in unique_parameter:
                        local_fitted_parameter[key].value=ta_local.par.value
        except:
                pass
        ta_local.par=local_fitted_parameter
        for key in ta_local.par.keys():
                ta_local.par[key].vary=False
        ta_local.Fit_Global()
        ta_local.Plot_Fit_output()
```

--------------------------------

### self.Compare_at_time()

Source: https://kimopack.readthedocs.io/en/latest/Comparing.html

Plots multiple spectra into the same figure at one or multiple given timepoints, supporting normalization and scaling.

```APIDOC
## self.Compare_at_time()

### Description
Plots multiple spectra into the same figure at one or multiple given timepoints (rel_time). It supports normalization and scaling, and can integrate over a time window if ta.time_width_percent is specified.

### Usage
This function is useful for comparing spectra across different solvents, quenchers, or fits. It also supports comparing measured spectra against external data loaded into a DataFrame.
```

--------------------------------

### Define Normalization Window

Source: https://kimopack.readthedocs.io/en/latest/_sources/Comparing.rst.txt

Specify the time and wavelength range for normalization using a four-element list.

```python
[Start time, End time, Start wavelength, End Wavelength]
```

--------------------------------

### self.Save_project()

Source: https://kimopack.readthedocs.io/en/latest/_sources/Saving.rst.txt

Saves the current TA project state as an HDF5 file for future reloading.

```APIDOC
## self.Save_project()

### Description
Saves the TA project as an HDF5 file, including set parameters, fit results, and raw data. It restores chirp-corrected data upon import. Note: External fit functions (ta.mod) must be re-assigned after reloading.

### Parameters
- **filename** (str) - Optional - The name of the file to save. If empty, defaults to the original ASCII filename.
- **path** (str) - Optional - The directory path for the saved file.
```

--------------------------------

### Save/Export Data as ASCII

Source: https://kimopack.readthedocs.io/en/latest/Saving.html

Exports raw and fit data to text files. Allows configuration of separators, file paths, and specific dataset selection.

```python
self.Save_data()
```

--------------------------------

### self.Save_Powerpoint()

Source: https://kimopack.readthedocs.io/en/latest/_sources/Saving.rst.txt

Generates a PowerPoint presentation containing slides for RAW plots and fit outputs.

```APIDOC
## self.Save_Powerpoint()

### Description
Calls 'Plot_RAW' and 'Plot_fit_output' to save plots as 'png' and compiles them into a PowerPoint file with separate slides for RAW and Fit data. If 'savetype' includes 'png', 'svg', or 'pdf', a summary file is also created.

### Parameters
- Parameters are identical to the plotting functions.
- **save_RAW** (bool) - Optional - Switch for faster processing of RAW plots.
- **save_Fit** (bool) - Optional - Switch for faster processing of Fit plots.
```

--------------------------------

### Parameter Naming Convention

Source: https://kimopack.readthedocs.io/en/latest/_sources/Fitting.rst.txt

The regex pattern required for naming parameters.

```regex
[a-z_][a-z0-9_]*
```

--------------------------------

### Recalculate DAS for Multiple Projects

Source: https://kimopack.readthedocs.io/en/latest/_sources/Fitting.rst.txt

Updates parameter values across a list of projects and triggers a global fit for each.

```python
for ta_local in projects_list:
	local_fitted_parameter=ta.par_fit
	try:
		for key in unique_parameter:
			local_fitted_parameter[key].value=ta_local.par.value
	except:
		pass
	ta_local.par=local_fitted_parameter
	for key in ta_local.par.keys():
		ta_local.par[key].vary=False
	ta_local.Fit_Global()
	ta_local.Plot_Fit_output()
```

--------------------------------

### Perform Global Fitting

Source: https://kimopack.readthedocs.io/en/latest/Fitting.html

Execute global fitting across multiple projects with optional weighting or shared DAS.

```python
ta.Fit_Global(multi_project = ta_list, unique_parameter = ‘pump_power’) ta.Fit_Global(multi_project = ta_list, unique_parameter = ‘pump_power’, weights = [1/power1,1/power2])
```

```python
ta.Fit_Global(multi_project=[ta1],same_DAS=True)
```

--------------------------------

### Save Plots as Powerpoint

Source: https://kimopack.readthedocs.io/en/latest/Saving.html

Generates a PowerPoint presentation with slides for raw and fit plots. Supports additional switches for faster processing.

```python
self.Save_Powerpoint()
```

--------------------------------

### self.Save_Powerpoint()

Source: https://kimopack.readthedocs.io/en/latest/Saving.html

Convenience function that saves plots as PNGs and creates a PowerPoint presentation.

```APIDOC
## self.Save_Powerpoint()

### Description
Convenience function that calls both “Plot_RAW” and if possible “Plot_fit_output” and saves the plots as “png”. It then creates a power point file with one slide for the RAW plots and one slide for the Fits. Additional switches save_RAW and save_Fit allow for faster processing.
```

--------------------------------

### Trigger Global Fit

Source: https://kimopack.readthedocs.io/en/latest/Fitting.html

Executes the global fitting process using the current parameter configuration.

```python
self.Fit_Global()
```

--------------------------------

### Iterative Global Fitting

Source: https://kimopack.readthedocs.io/en/latest/Fitting.html

Refine fit parameters iteratively, useful for chirp optimization.

```python
for i in range(5):
        start_error=ta.re['error']
        ta.par=ta.par_fit
        ta.Fit_Global(fit_chirp=True)
        if not ta.re['error'] < start_error:break
```

--------------------------------

### Accessing multi-project results

Source: https://kimopack.readthedocs.io/en/latest/_sources/Fitting.rst.txt

Retrieve and plot results from specific projects stored in the multi_projects variable after a global fit.

```python
ta.re = ta.multi_projects[1] 
ta.Plot_fit_output()
```

```python
ta.re = ta.multi_projects[0]
```

--------------------------------

### self.Plot_fit_output()

Source: https://kimopack.readthedocs.io/en/latest/Plotting.html

Plots the fit results using data from shaped and cut datasets, including rebinning and temporal restrictions.

```APIDOC
## self.Plot_fit_output()

### Description
Plots the fit results using the data contained in the shaped and cut datasets that were used for the fit. This includes all rebinning or temporal restrictions applied to the model.

### Usage
`self.Plot_fit_output()`

### Plot Contents
- **DAC**: Assigned spectra for each component (DAS for independent exponential decays, SAS for other models).
- **Summed Intensity**: Sum of all wavelengths for both data and fit.
- **Kinetics**: Plot kinetics for selected wavelengths.
- **Spectra**: Plot spectra at selected times.
- **Matrix**: Plots measured, modelled, and error matrices (supports 'error_matrix_amplification' scaling factor).
- **Concentrations**: Relative concentrations of species as a function of time.
```

--------------------------------

### Access Multi-Project Results

Source: https://kimopack.readthedocs.io/en/latest/Fitting.html

Retrieve and plot results from specific projects when using same_DAS=True.

```python
ta.re = ta.multi_projects[1]
ta.Plot_fit_output()
```

```python
ta.re = ta.multi_projects[0]
```

--------------------------------

### Resetting shaping parameters

Source: https://kimopack.readthedocs.io/en/latest/_sources/Shaping.rst.txt

Explicitly reset a parameter to None to clear previous settings, as commenting out a line does not revert to default values.

```python
ta.intensity_range = 3e-3 
#ta.intensity_range = 3e-3 #no effect
ta.intensity_range = None
```

--------------------------------

### Global fitting with shared DAS

Source: https://kimopack.readthedocs.io/en/latest/_sources/Fitting.rst.txt

Perform global fitting while enforcing the same Decay Associated Spectra (DAS) across projects.

```python
ta.Fit_Global(multi_project=[ta1],same_DAS=True)
```

--------------------------------

### Parameter Name Regex Pattern

Source: https://kimopack.readthedocs.io/en/latest/_sources/Fitting.rst.txt

Regex pattern used to validate parameter names.

```regex
[a-z_][a-z 0-9_]*
```

--------------------------------

### Resetting Data Parameters

Source: https://kimopack.readthedocs.io/en/latest/Shaping.html

Explicitly set a parameter to None to revert it, as commenting out a line does not reset the value to its default.

```python
ta.intensity_range = 3e-3
#ta.intensity_range = 3e-3 #no effect
ta.intensity_range = None
```

--------------------------------

### Rate Parameter Recognition Logic

Source: https://kimopack.readthedocs.io/en/latest/_sources/Fitting.rst.txt

Python logic used to determine if a parameter is interpreted as a rate based on its name.

```python
bool(re.match(re.compile(’[k]'̣), parameter_name[:2])
```

--------------------------------

### self.Save_data()

Source: https://kimopack.readthedocs.io/en/latest/_sources/Saving.rst.txt

Exports data to ASCII/text format for use in external plotting programs.

```APIDOC
## self.Save_data()

### Description
Exports chirp-corrected data, slices, and fit results to ASCII/text files. Automatically generates a text file containing fit results.

### Parameters
- **save_RAW** (bool) - Optional - Selects if RAW datasets are stored.
- **save_Fit** (bool) - Optional - Selects if Fit datasets are stored.
- **save_slices** (bool) - Optional - Selects if slices defined by ta.rel_wave and ta.rel_time are saved.
- **save_binned** (bool) - Optional - Selects if the chirp-corrected and rebinned dataset is saved.
- **filename** (str) - Optional - Base filename for exported files.
- **path** (str) - Optional - Folder path relative to ta.path.
- **sep** (str) - Optional - Separator used for values (default is 'TAP').
```

--------------------------------

### Extract and Plot Species Spectra

Source: https://kimopack.readthedocs.io/en/latest/_sources/Fitting.rst.txt

Extracts species spectra and subtracts specific contributions before plotting the raw data.

```python
#extract the spectra
dicten=pf.Species_Spectra(ta) 
#plot the measured spectrum and substract the 
#contribution of "1" and "2"
ta.Plot_RAW(ds=ta.re['A']-dicten[1]-dicten[2])
```

--------------------------------

### Iterative Global Fitting

Source: https://kimopack.readthedocs.io/en/latest/_sources/Fitting.rst.txt

Refines fit results by iteratively updating parameters and re-running the global fit until the error stops decreasing.

```python
for i in range(5):
	start_error=ta.re['error']
	ta.par=ta.par_fit
	ta.Fit_Global(fit_chirp=True)
	if not ta.re['error'] < start_error:break
```

--------------------------------

### Save Plots

Source: https://kimopack.readthedocs.io/en/latest/Saving.html

Convenience function to save both raw and fit plots. Parameters are passed through to the underlying plotting functions.

```python
self.Save_Plots()
```

--------------------------------

### Manual data filtering

Source: https://kimopack.readthedocs.io/en/latest/_sources/Shaping.rst.txt

Directly manipulate the dataset matrix to filter out values exceeding a specific threshold.

```python
ta.ds (the chirp corrected data) or ta.ds_ori[ta.ds_ori>20]=0 is the classical way to filter
```

--------------------------------

### self.Save_Plots()

Source: https://kimopack.readthedocs.io/en/latest/_sources/Saving.rst.txt

A convenience function that triggers both Plot_RAW and Plot_fit_output to save current plots for status capture.

```APIDOC
## self.Save_Plots()

### Description
Calls both 'Plot_RAW' and 'Plot_fit_output' (if available) to save the current plots. This is intended for quick exploratory work to capture the current status.

### Parameters
- Parameters are identical to the underlying 'Plot_RAW' and 'Plot_fit_output' functions.
```

--------------------------------

### Scale Data Intensity

Source: https://kimopack.readthedocs.io/en/latest/_sources/Comparing.rst.txt

Manually adjust the intensity of a dataset by modifying the internal data matrix. Note that this modifies the current object's data, but the original data remains preserved in ta.ds_ori.

```python
"ta.ds*=1.1"
```
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