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Conversion factors from um to nanometre added in load_gwy in io.py #659

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Commits on Sep 9, 2023

  1. SI Unit of um and mm for gwy added

    Some of .gwy files raise ValueError in io.py.
    
    ValueError: Units 'um' have not been added for .gwy files
    iobataya committed Sep 9, 2023
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Commits on Sep 10, 2023

  1. Correct Loading gwy channels and units

    # XY, Z units correction
    * units for px_to_nm to multiply data array should be picked up from 'si_unit_z' instetad of 'si_unit_xy'.
    * Non-square image should be considered. Probably, px_to_nm_z, px_to_nm_x, px_to_nm_y will be necessary.
    
    # Channel index
    Data key of gwy sometimes starts from 1 or larger. (ex. '/4/data') It happens when image is cropped on Gwyddion, and it remains after saving even other channels are removed.
    
    A loop to scan indices was added. And it guesses whether if the channel is topography or not by si_unit_z.
    iobataya committed Sep 10, 2023
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Commits on Sep 11, 2023

  1. Update io.py

    Unit is set during scanning of channel index.
    iobataya committed Sep 11, 2023
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  2. LoadScans gwyddion routines updated

    # transposed np.ndarray corrected
    _gwy_read_component returns transposed dimensions of (xres,yres), this corrected to (yres, xres)
    
    # load_gwy updated
    * load_gwy can find multichannel data starting from any index (ex. 4/data)
    * load_gwy can guess whether if it is height channel by unitstr
    * load_gwy supports m,mm,um for z-unit
    * px_to_nm_x, px_to_nm_y were added for future usage, stored in img_dict
    iobataya committed Sep 11, 2023
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Commits on Sep 15, 2023

  1. io.py and testing added

    io.py modified
     - Conversion from gwy.DataField to np.ndarray was corrected.
       (dimension was transposed)
     - Scale class added to conversion of units and holds conversion factors
       - Initializable by configuration YAML file
       - This object is copied to img_dict of data
          accessible scan.img_dict[filename]["scale"]
          px_to_nm_x, px_to_nm_y values in img_dict from Gwy
    
    Testing and Configurations
     - Resource files (file_landscape.gwy, file.square.gy) added.
     - conftest.py modified to read file.gwy and file_landscape.gwy
     - Test for Scale class
        - test_scale_config was added.
        - test_scale in test_io.py was added.
    - "scale" configuration was added to default_config.yaml
    iobataya committed Sep 15, 2023
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  3. Format corrected

    iobataya committed Sep 15, 2023
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Commits on Sep 27, 2023

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