# Comparisons

Users must switch to the comparison page. Go to the action menu bar and navigate
to "File → Perform comparisons from a remote sensing instrument" as seen in [Figure 15](#fig-15).

```{eval-rst}
.. figure:: ../../images/user_guide/action_to_comparisons.png
   :name: fig-15
   :align: center
   :alt: Action menu option to switch to the comparisons page

   Action menu option to switch to the comparisons page.
```

## Comparison Input

```{eval-rst}
.. figure:: ../../images/user_guide/initial_comparison_page.png
   :name: fig-16
   :align: center
   :alt: Initial view of the comparison page

   Initial view of the comparison page.
```

The comparison page ([Figure 16](#fig-16)) contains the user input fields at the top:
- **Lunar Observation Files**:
  - Instrument observation netCDF files in GLOD format to be compared.
    - GLOD formats are explained in the [File Formats](./formats.md) section.
  - "LOAD FILES": Opens a file selection dialog for loading observation files.
  - "UNLOAD FILES": Clears all loaded observation files.
- **SRF File**:
  - SRF netCDF file in GLOD format.
    - Must contain channels matching those in the observation files.
  - "LOAD FILE": Opens a file selection dialog for selecting the SRF file.
- **Compare Button**:
  - Initiates the comparison processing, displaying a progress indicator (as shown in [Figure 17](#fig-17)).
  - This button is enabled once valid observations and an SRF file are loaded.

```{eval-rst}
.. figure:: ../../images/user_guide/processing_comparison_page.png
   :name: fig-17
   :align: center
   :alt: Comparison page processing comparisons

   Comparison page processing comparisons.
```

## Comparison Output

Once comparisons are computed, the comparison page presents the results and
provides tools for exploring the data, as shown in [Figure 18](#fig-18).

```{eval-rst}
.. figure:: ../../images/user_guide/comparison_finished.png
   :name: fig-18
   :align: center
   :alt: Comparison page after comparisons are computed

   Comparison page after comparisons are computed.
```

### Default View
- The **instrument’s first-channel irradiance observations** (blue) are plotted alongside  
  **LIME simulations** (orange) for the same channel.
- The **x-axis** represents the **comparison variable** (default: **Date**).
- The **primary y-axis** represents **irradiance values**.
- The **secondary y-axis** (right) represents the **relative difference (%)** (gray).

### User Options
- **Channel Selection**: Switch between instrument channels via the "Channels" tab (above the graphs).
- **Difference Metric**: Adjust the displayed difference via the "Difference" dropdown (top-right), selecting:
  - **Relative difference**
  - **Percentage difference**
  - **No difference**
- **Comparison Method**: Change the comparison basis via the "Comparison by" dropdown (top-center) from **Date** to:
  - **Moon phase angle**
  - **Wavelength**, with two visualization options:
    - **Mean-based Comparison**: Computes the mean of all observations and simulations for each channel.
    - **Boxplot Visualization**: Displays the distribution of values per channel, as explained in [Figure 19](#fig-19).
- **New Comparison**: Click "NEW" (top-left) to clear results and start a new comparison.  
  - A **confirmation dialog** appears, as shown in [Figure 20](#fig-20).

```{eval-rst}
.. figure:: ../../images/user_guide/boxplot_meaning.png
   :name: fig-19
   :align: center
   :alt: LIME comparisons boxplots dissected

   Breakdown of LIME comparison boxplots.
```

```{eval-rst}
.. figure:: ../../images/user_guide/clear_comparison.png
   :name: fig-20
   :align: center
   :alt: Dialog asking for confirmation after clicking \"NEW\"

   Dialog asking for confirmation after clicking "NEW"
```


### Exporting Data
- Graphs can be exported as images (JPG, PNG, PDF, etc.) or CSV files.
- The full comparison dataset can be saved as a netCDF file, allowing it to be reloaded in LIME Toolbox for future analysis.

## Comparing throught the Command-Line Interface (CLI)

### CLI Comparison Input

To perform comparisons via CLI, use the `-c` or `--comparison` option along with `-f` or `--srf`:
```sh
lime -c "path_observation_1 path_observation_2 ... path_observation_n" -f path_srf
```

**Example:**
To compare `input_1.nc`, `input_2.nc` and `input_3.nc`, using the spectral response function
defined in `srf.nc`:
```sh
lime -c "input_1.nc input_2.nc input_3.nc" -f srf.nc
```

Users can also use glob patterns to load multiple files.
For example to compare all `.nc` files in the `files` directory:
```sh
lime -c "files/*.nc" 
```

### CLI Comparison Output

As with simulations, comparison results must be be exported in order to be able to interact
with them. Append the `-o` or `--output` option for this.

#### Graphical Export (Image/PDF)
Specify the image type, comparison variable, difference metric, and file paths for each channel:
```sh
-o graph,(pdf|jpg|png|svg),(DT|MPA|BOTH|CHANNEL|CHANNEL_MEAN),(rel|perc|none),comparison_channel_1,comparison_channel_2,...,comparison_channel_n
```
To simplify, export all channels to a directory using `graphd`:
```sh
-o graphd,(pdf|jpg|png|svg),(DT|MPA|BOTH|CHANNEL|CHANNEL_MEAN),(rel|perc|none),output_directory
```

**Examples:**
```sh
-o graph,jpg,DT,rel,comparison1.jpg,comparison2.jpg
```
Using `graphd`:
```sh
-o graphd,jpg,DT,rel,comparison_dir
```

#### Data Export (CSV File)
Specify the comparison variable, difference metric, and file paths for each channel:
```sh
-o csv,(DT|MPA|BOTH|CHANNEL|CHANNEL_MEAN),(rel|perc|none),comparison_channel_1,comparison_channel_2,...,comparison_channel_n
```
To export all channels to a directory, use `csvd`:
```sh
-o csvd,(DT|MPA|BOTH|CHANNEL|CHANNEL_MEAN),(rel|perc|none),output_directory
```

**Examples:**
```sh
-o csv,DT,rel,comparison1.csv,comparison2.csv
```
Using `csvd`:
```sh
-o csvd,DT,rel,comparison_dir
```

#### NetCDF Export
Specify the netCDF file path:
```sh
-o nc,output_path
```

**Example:**
```sh
-o nc,output.nc
```