Merge branch 'master' of github.com:MShirazAhmad/PhysPlot

Author: MShirazAhmad

README.md

@@ -6,34 +6,60 @@
 
 PhysPlot is a scientific plotting software with a graphical user interface, designed to produce publication-ready 2D plots. It supports vector and bitmap output, including PDF, Postscript, SVG and EPS. It allows data to be imported from text, CSV and Excel files and It can export data in text format. Datasets can also be entered within the program, and new datasets can be created via the manipulation of existing datasets using mathematical expressions.
 
-## License, Tutorials, and Contributions
+## Quick Start (from source)
 
-PhysPlot source code is licensed under the PolyForm Noncommercial License 1.0.0. You may fork PhysPlot, study the code, make noncommercial improvements, and submit revisions back through pull requests.
+Clone the repository:
 
-Commercial use is not allowed without prior written permission from the project originator.
+```bash
+git clone https://github.com/MShirazAhmad/PhysPlot.git
+cd PhysPlot
+```
 
-Documentation, screenshots, tutorials, website text, walkthroughs, and educational media are licensed under Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) unless otherwise stated. Noncommercial tutorials and educational guides are welcome.
+Create and activate a virtual environment:
 
-The PhysPlot name, logo, app icon, GUI branding, and official visual identity are reserved by the project originator. Unofficial forks or modified builds must not be presented as official PhysPlot releases.
+```bash
+python -m venv .venv
+```
 
-Only pull requests merged by the maintainer are official PhysPlot revisions. For details, see [CONTRIBUTING.md](CONTRIBUTING.md) and [TRADEMARK.md](TRADEMARK.md).
+On macOS/Linux:
+
+```bash
+source .venv/bin/activate
+```
 
-# Pictorial procedure for data analysis
+On Windows (PowerShell):
 
-![Image description](pictorial_procedure/PP2.png)
+```powershell
+.venv\Scripts\Activate.ps1
+```
 
-![Image description](pictorial_procedure/PP3.png)
+Install dependencies:
 
-![Image description](pictorial_procedure/PP4.png)
+```bash
+python -m pip install --upgrade pip
+python -m pip install -r requirements.txt
+```
 
-![Image description](pictorial_procedure/PP5.png)
+Run PhysPlot:
 
-![Image description](pictorial_procedure/PP6.png)
+```bash
+python PhysPlot.py
+```
 
-![Image description](pictorial_procedure/PP7.png)
+Alternative module entry point:
 
-![Image description](pictorial_procedure/PP8.png)
+```bash
+python -m physplot
+```
 
-![Image description](pictorial_procedure/PP9.png)
+## License, Tutorials, and Contributions
 
-![Image description](pictorial_procedure/PP10.png)
+PhysPlot source code is licensed under the PolyForm Noncommercial License 1.0.0. You may fork PhysPlot, study the code, make noncommercial improvements, and submit revisions back through pull requests.
+
+Commercial use is not allowed without prior written permission from the project originator.
+
+Documentation, screenshots, tutorials, website text, walkthroughs, and educational media are licensed under Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) unless otherwise stated. Noncommercial tutorials and educational guides are welcome.
+
+The PhysPlot name, logo, app icon, GUI branding, and official visual identity are reserved by the project originator. Unofficial forks or modified builds must not be presented as official PhysPlot releases.
+
+Only pull requests merged by the maintainer are official PhysPlot revisions. For details, see [CONTRIBUTING.md](CONTRIBUTING.md) and [TRADEMARK.md](TRADEMARK.md).

docs/extensions/curvefitting.rst

@@ -23,6 +23,12 @@ If your plotted data looks like a line, choose a linear fit. If your plotted
 data follows exponential decay, choose an exponential model. A curve-fitting
 plugin is simply a small file that tells PhysPlot what equation to use.
 
+Where Curve Fits Appear in the UI
+---------------------------------
+
+Discovered curve-fitting plugins are listed in the curve-fit configuration
+window. PhysPlot discovers these files at startup.
+
 Required File Location
 ----------------------
 
@@ -87,7 +93,19 @@ Callable Template
        Returns:
            numpy.ndarray: Model Y values for the input X array.
        """
-       return amplitude * np.exp(-((x - center) / width) ** 2)
+        return amplitude * np.exp(-((x - center) / width) ** 2)
+
+Step-by-Step: Build a New Curve-Fit Plugin
+------------------------------------------
+
+1. Create a new file in ``curvefitting/`` (for example
+   ``curvefitting/12_gaussian.py``).
+2. Add ``DISPLAY_NAME``, ``DEFAULT_LABEL``, ``KIND``, and ``LABEL_MODES``.
+3. For ``KIND = "poly"``, add ``DEGREE``.
+4. For ``KIND = "callable"``, implement ``function(x, ...)`` and optionally
+   add ``INITIAL_GUESS``.
+5. Restart PhysPlot so the new fit appears in the curve-fit list.
+6. Select the fit in the configuration window and apply it to plotted data.
 
 Required Fields
 ---------------

docs/extensions/fileloading.rst

@@ -8,6 +8,17 @@ File-loader plugins convert external data files into a two-dimensional table
 that PhysPlot can display. A loader receives a file path and returns a
 rectangular data array.
 
+Where Loaders Appear in the UI
+------------------------------
+
+Discovered loaders are shown in two places:
+
+- **Settings > File Loader** (menu selection)
+- **Data Loader** dropdown above the **Import Data** button (quick selection)
+
+The selected loader is used when importing files. PhysPlot discovers loader
+files at startup.
+
 Layman Example
 --------------
 
@@ -81,7 +92,31 @@ Minimal CSV-Like Template
            if len(parts) < 2:
                continue
            rows.append((float(parts[0]), float(parts[1])))
-       return np.asarray(rows, dtype=float)
+        return np.asarray(rows, dtype=float)
+
+Step-by-Step: Build a New Loader
+--------------------------------
+
+1. Create a new file in ``fileloader/`` (for example
+   ``fileloader/my_device_loader.py``).
+2. Define a human-readable ``title`` string.
+3. Implement ``load_data(file_path)`` to parse your format and return a 2D
+   array-like result.
+4. Optionally define ``DEFAULT_COLUMN_ROLES`` to pre-assign column roles after
+   import.
+5. Restart PhysPlot so the loader is discovered and added to the menu and
+   dropdown.
+6. Select your loader from **Settings > File Loader** or the **Data Loader**
+   dropdown, then import a file.
+
+Loader Categories
+-----------------
+
+- **General tabular loader**: parse delimited numeric files.
+- **Instrument-specific loader**: skip custom headers/metadata and keep
+  meaningful columns.
+- **Role-aware loader**: also sets ``DEFAULT_COLUMN_ROLES`` for automatic
+  X/Y mapping.
 
 OES HRF Pattern
 ---------------

docs/extensions/functions.rst

@@ -16,6 +16,16 @@ PhysPlot reads the input column as a one-dimensional numeric array, calls the
 plugin's ``transform(values)`` function, then writes the returned values into
 the output column.
 
+Where Functions Appear in the UI
+--------------------------------
+
+Discovered function plugins are available in:
+
+- The top-bar **Functions** menu
+- The transform dropdown in the data-manipulation controls
+
+PhysPlot discovers function files at startup.
+
 Layman Example
 --------------
 
@@ -82,7 +92,28 @@ Minimal Template
        maximum = np.nanmax(values)
        if maximum == minimum:
            return np.zeros_like(values)
-       return (values - minimum) / (maximum - minimum)
+        return (values - minimum) / (maximum - minimum)
+
+Step-by-Step: Build a New Function
+----------------------------------
+
+1. Create a new file in ``functions/`` (for example
+   ``functions/15_normalize.py``).
+2. Define ``DISPLAY_NAME`` for the GUI entry.
+3. Define ``DEFAULT_LABEL`` for generated labels.
+4. Implement ``transform(values)`` and return one value per input row.
+5. Restart PhysPlot so the function appears in the menu and dropdown.
+
+Function Categories
+-------------------
+
+Common categories used by PhysPlot plugins include:
+
+- **Identity/basic**: pass-through operations.
+- **Power/reciprocal**: ``x^2``, ``x^3``, ``1/x``.
+- **Log/exp**: ``log10``, ``ln``, ``e^x``.
+- **Trigonometric**: ``sin``, ``cos``, ``tan``, inverse trig.
+- **Domain-specific**: custom transforms such as baseline correction.
 
 Practical Rules
 ---------------

docs/index.rst

@@ -4,10 +4,44 @@ PhysPlot: Advanced Plotting Made Simple
 .. image:: _static/PhysPlotWide.png
    :alt: PhysPlot logo
    :align: center
-   :width: 420px
+   :width: 620px
 
 PhysPlot is a scientific plotting software with a graphical user interface, designed to produce publication-ready 2D plots. It supports vector and bitmap outputs and allows importing, transforming, plotting, fitting, and exporting datasets.
 
+Branding
+--------
+
+PhysPlot documentation uses the official wide brand asset ``_static/PhysPlotWide.png`` on the home page and follows the project trademark policy for name and logo usage.
+
+Plugin System
+-------------
+
+PhysPlot supports plugin-based extension points for importing, transforming, and fitting data without editing core GUI files.
+
+File Loader plugins
+~~~~~~~~~~~~~~~~~~~
+
+- Add ``.py`` files to ``fileloader/`` with ``title`` and ``load_data(file_path)``.
+- The default loader keeps CSV/XLSX/TXT/TSV support.
+- Loaders are auto-discovered and appear in both:
+
+  - **Settings > File Loader**
+  - The **Data Loader** dropdown above **Import Data**
+
+Transform Function plugins
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- Add ``.py`` files to ``functions/`` with ``DISPLAY_NAME``, ``DEFAULT_LABEL``, and ``transform(values)``.
+- Built-in transform categories include identity, powers, reciprocal, logarithmic, exponential, and trigonometric operations.
+- Functions are auto-discovered and shown in the top-bar **Functions** menu and transform dropdown.
+
+Curve-Fitting plugins
+~~~~~~~~~~~~~~~~~~~~~
+
+- Add ``.py`` files to ``curvefitting/`` for polynomial or callable models.
+- Files are discovered at startup and shown in the curve-fit configuration list.
+- Use this for custom equations and domain-specific fitting workflows.
+
 Project links
 -------------
 

docs/installation.rst

@@ -7,20 +7,40 @@ Prerequisites
 - Python 3.7 or newer
 - pip
 
-Usage modes
------------
+Clone the repository
+--------------------
 
-PhysPlot is available in two common modes:
+.. code-block:: bash
+
+   git clone https://github.com/MShirazAhmad/PhysPlot.git
+   cd PhysPlot
+
+Create and activate a virtual environment
+-----------------------------------------
+
+.. code-block:: bash
+
+   python -m venv .venv
+
+On macOS/Linux:
+
+.. code-block:: bash
+
+   source .venv/bin/activate
+
+On Windows (PowerShell):
+
+.. code-block:: powershell
 
-1. Packaged desktop builds when provided by the official PhysPlot project.
-2. Python script execution using ``PhysPlot.py``.
+   .venv\Scripts\Activate.ps1
 
 Install Python dependencies
 ---------------------------
 
 .. code-block:: bash
 
-   pip install PyQt5 matplotlib numpy scipy pandas
+   python -m pip install --upgrade pip
+   python -m pip install -r requirements.txt
 
 Run PhysPlot
 ------------
@@ -31,5 +51,11 @@ From the project directory:
 
    python PhysPlot.py
 
+Alternative module entry point:
+
+.. code-block:: bash
+
+   python -m physplot
+
 Keep the ``physplot/inc`` image assets with the source tree so the GUI can load
 the official app icon and logo.

docs/user_guide/data_import.rst

@@ -6,8 +6,20 @@ Supported formats
 
 - ``.txt``
 - ``.csv``
+- ``.tsv``
 - ``.xlsx``
 
+Loader selection
+----------------
+
+PhysPlot uses plugin-based file loaders. You can choose the active loader from:
+
+- **Settings > File Loader**
+- The **Data Loader** dropdown above **Import Data**
+
+Loader plugins are auto-discovered at startup from the ``fileloader/`` folder.
+The built-in default loader keeps standard CSV/XLSX/TXT/TSV import support.
+
 Import steps
 ------------