.. _ia_workflow:

Example walkthrough
-------------------

.. _step1:

1. Click :guilabel:`Open` button in the upper left corner. 
   Navigate to location of image file and open the file. The :ref:`source image <ia_source_image>` will be displayed
   in the top left image panel. 

   .. figure:: /images/ia/i_0.png
      :alt: i/i_0
      :width: 500px
      :align: center
  
   .. note:: 
      The relevant part of the image is automatically selected, but manual :ref:`selection adjustment <ia_crop>` may be needed.
             
   .. hint::
      Use the mouse scroll-wheel to zoom in and out of any of the images; the little :guilabel:`A` button in the lower left resets the zoom.

   

2. The program displays the :ref:`selected edges <ia_absorbance>`
   automatically. Adjustable green boxes are overlaid over the selected edges.

   .. note:: 
      Make  sure make sure the edges are selected correctly by the green boxes.
      The green boxes can be :ref:`manually resized and/or re-positioned <ia_edge_selection>`.

   .. figure:: /images/ia/edge_selection.png
      :alt: edge_selection
      :width: 500px
      :align: center

3. Select the :ref:`sample edge type <ia_sample_type>` based on your particular sample configuration. 

4. Once image cropped properly, click :guilabel:`Compute` in upper left corner. The fitted edge polynomials
   will be displayed in the :ref:`Edge panels <ia_edge_result>`. 

   .. note:: 
      You may need to adjust the :ref:`fit threshold <ia_fit_theshold>` for edges with non-uniform contrast. 

   .. note:: Ideally the edges should be fit with a polynomial of order 1 or 2. 
      However if the edge is not straight you can try to use a :ref:`higher order polynomial <ia_poly_order>`.
     
   .. figure:: /images/ia/edges_fitted.png
      :alt: edges_fitted
      :width: 600px
      :align: center

5. The thickness of the sample and standard deviation are displayed at the top of the 
   window in the units of number of pixels. 


6. Repeat steps 1-5 for each image that you recorded. 

   .. note:: Other files in the same folder can be selected by clicking on other filenames in the :ref:`File list <ia_file_list>` in left panel. No need to click :guilabel:`Open` button to load each file.

7. Click :guilabel:`Save results` button to export the calculate distances and uncertainties to a ``.csv`` file.