mapreader.load.images

Module Contents

Classes

MapImages

Class to manage a collection of image paths and construct image objects.
class mapreader.load.images.MapImages(path_images=None, file_ext=False, tree_level='parent', parent_path=None, **kwargs)

Class to manage a collection of image paths and construct image objects.

Parameters:

  • path_images (str or None, optional) – Path to the directory containing images (accepts wildcards). By default, False

  • file_ext (str or False, optional) – The file extension of the image files to be loaded, ignored if file types are specified in path_images (e.g. with "./path/to/dir/*png"). By default False.

  • tree_level (str, optional) – Level of the image hierarchy to construct. The value can be "parent" (default) and "patch".

  • parent_path (str, optional) – Path to parent images (if applicable), by default None.

  • **kwargs (dict, optional) – Additional keyword arguments to be passed to the _images_constructor method.

path_images

List of paths to the image files.

Type:

list

images

A dictionary containing the constructed image data. It has two levels of hierarchy, "parent" and "patch", depending on the value of the tree_level parameter.

Type:

dict

add_metadata(metadata, index_col=0, delimiter=',', columns=None, tree_level='parent', ignore_mismatch=False)

Add metadata information to the images dictionary.

Parameters:

  • metadata (str or pandas.DataFrame) – Path to a csv (or similar), xls or xlsx file or a pandas DataFrame that contains the metadata information.

  • index_col (int or str, optional) –

    Column to use as the index when reading the file and converting into a panda.DataFrame. Accepts column indices or column names. By default 0 (first column).

    Only used if a file path is provided as the metadata parameter. Ignored if columns parameter is passed.

  • delimiter (str, optional) –

    Delimiter used in the csv file, by default ",".

    Only used if a csv file path is provided as the metadata parameter.

  • columns (list, optional) – List of columns indices or names to add to MapImages. If None is passed, all columns will be used. By default None.

  • tree_level (str, optional) – Determines which images dictionary ("parent" or "patch") to add the metadata to, by default "parent".

  • ignore_mismatch (bool, optional) – Whether to error if metadata with mismatching information is passed. By default False.

Raises:

ValueError –

If metadata is not a pandas DataFrame or a csv, xls or xlsx file path.

If ‘name’ or ‘image_id’ is not one of the columns in the metadata.

Return type:

None

Notes

Your metadata file must contain an column which contains the image IDs (filenames) of your images. This should have a column name of either name or image_id.

Existing information in your MapImages object will be overwritten if there are overlapping column headings in your metadata file/dataframe.

show_sample(num_samples, tree_level='patch', random_seed=65, **kwargs)

Display a sample of images from a particular level in the image hierarchy.

Parameters:

  • num_samples (int) – The number of images to display.

  • tree_level (str, optional) – The level of the hierarchy to display images from, which can be "patch" or "parent". By default “patch”.

  • random_seed (int, optional) – The random seed to use for reproducibility. Default is 65.

  • **kwargs (dict, optional) – Additional keyword arguments to pass to matplotlib.pyplot.figure().

Returns:

The figure generated

Return type:

matplotlib.Figure

list_parents()

Return list of all parents

Return type:

list[str]

list_patches()

Return list of all patches

Return type:

list[str]

add_shape(tree_level='parent')

Add a shape to each image in the specified level of the image hierarchy.

Parameters:

tree_level (str, optional) – The level of the hierarchy to add shapes to, either "parent" (default) or "patch".

Return type:

None

Notes

The method runs mapreader.load.images.MapImages._add_shape_id() for each image present at the tree_level provided.

add_coords_from_grid_bb(verbose=False)
Parameters:

verbose (bool)

Return type:

None

add_coord_increments(verbose=False)

Adds coordinate increments to each image at the parent level.

Parameters:

verbose (bool, optional) – Whether to print verbose outputs, by default False.

Return type:

None

Notes

The method runs mapreader.load.images.MapImages._add_coord_increments_id() for each image present at the parent level, which calculates pixel-wise delta longitude (dlon) and delta latitude (dlat) for the image and adds the data to it.

add_patch_coords(verbose=False)

Add coordinates to all patches in patches dictionary.

Parameters:

verbose (bool, optional) – Whether to print verbose outputs. By default, False

Return type:

None

add_patch_polygons(verbose=False)

Add polygon to all patches in patches dictionary.

Parameters:

verbose (bool, optional) – Whether to print verbose outputs. By default, False

Return type:

None

add_center_coord(tree_level='patch', verbose=False)

Adds center coordinates to each image at the specified tree level.

Parameters:

  • tree_level (str, optional) – The tree level where the center coordinates will be added. It can be either "parent" or "patch" (default).

  • verbose (bool, optional) – Whether to print verbose outputs, by default False.

Return type:

None

Notes

The method runs mapreader.load.images.MapImages._add_center_coord_id() for each image present at the tree_level provided, which calculates central longitude and latitude (center_lon and center_lat) for the image and adds the data to it.

patchify_all(method='pixel', patch_size=100, tree_level='parent', path_save=None, add_to_parents=True, square_cuts=False, resize_factor=False, output_format='png', rewrite=False, verbose=False)

Patchify all images in the specified tree_level and (if add_to_parents=True) add the patches to the MapImages instance’s images dictionary.

Parameters:

  • method (str, optional) – Method used to patchify images, choices between "pixel" (default) and "meters" or "meter".

  • patch_size (int, optional) – Number of pixels/meters in both x and y to use for slicing, by default 100.

  • tree_level (str, optional) – Tree level, choices between "parent" or "patch, by default "parent".

  • path_save (str, optional) – Directory to save the patches. If None, will be set as f”patches_{patch_size}_{method}” (e.g. “patches_100_pixel”). By default None.

  • add_to_parents (bool, optional) – If True, patches will be added to the MapImages instance’s images dictionary, by default True.

  • square_cuts (bool, optional) – If True, all patches will have the same number of pixels in x and y, by default False.

  • resize_factor (bool, optional) – If True, resize the images before patchifying, by default False.

  • output_format (str, optional) – Format to use when writing image files, by default "png".

  • rewrite (bool, optional) – If True, existing patches will be rewritten, by default False.

  • verbose (bool, optional) – If True, progress updates will be printed throughout, by default False.

Return type:

None

calc_pixel_stats(parent_id=None, calc_mean=True, calc_std=True, verbose=False)

Calculate the mean and standard deviation of pixel values for all channels of all patches of a given parent image. Store the results in the MapImages instance’s images dictionary.

Parameters:

  • parent_id (str or None, optional) – The ID of the parent image to calculate pixel stats for. If None, calculate pixel stats for all parent images. By default, None

  • calc_mean (bool, optional) – Whether to calculate mean pixel values. By default, True.

  • calc_std (bool, optional) – Whether to calculate standard deviation of pixel values. By default, True.

  • verbose (bool, optional) – Whether to print verbose outputs. By default, False.

Return type:

None

Notes

  • Pixel stats are calculated for patches of the parent image specified by parent_id.

  • If parent_id is None, pixel stats are calculated for all parent images in the object.

  • If mean or standard deviation of pixel values has already been calculated for a patch, the calculation is skipped.

  • Pixel stats are stored in the images attribute of the MapImages instance, under the patch key for each patch.

  • If no patches are found for a parent image, a warning message is displayed and the method moves on to the next parent image.

convert_images(save=False, save_format='csv', delimiter=',')

Convert the MapImages instance’s images dictionary into pandas DataFrames for easy manipulation.

Parameters:

  • save (bool, optional) – Whether to save the dataframes as files. By default False.

  • save_format (str, optional) – If save = True, the file format to use when saving the dataframes. Options of csv (“csv”) or excel (“excel” or “xlsx”). By default, “csv”.

  • delimiter (str, optional) – The delimiter to use when saving the dataframe. By default ",".

Returns:

The method returns a tuple of two DataFrames: One for the parent images and one for the patch images.

Return type:

tuple of two pandas DataFrames

show_parent(parent_id, column_to_plot=None, **kwargs)

A wrapper method for .show() which plots all patches of a specified parent (parent_id).

Parameters:

  • parent_id (str) – ID of the parent image to be plotted.

  • column_to_plot (str, optional) – Column whose values will be plotted on patches, by default None.

  • **kwargs (Dict) – Key words to pass to show method. See help text for show for more information.

Returns:

A list of figures created by the method.

Return type:

list

Notes

This is a wrapper method. See the documentation of the mapreader.load.images.MapImages.show() method for more detail.

show(image_ids, column_to_plot=None, figsize=(10, 10), plot_parent=True, patch_border=True, border_color='r', vmin=None, vmax=None, alpha=1.0, cmap='viridis', discrete_cmap=256, plot_histogram=False, save_kml_dir=False, image_width_resolution=None, kml_dpi_image=None)

Plot images from a list of image_ids.

Parameters:

  • image_ids (str or list) – Image ID or list of image IDs to be plotted.

  • column_to_plot (str, optional) – Column whose values will be plotted on patches, by default None.

  • plot_parent (bool, optional) – If True, parent image will be plotted in background, by default True.

  • figsize (tuple, optional) – The size of the figure to be plotted. By default, (10,10).

  • patch_border (bool, optional) – If True, a border will be placed around each patch, by default True.

  • border_color (str, optional) – The color of the border. Default is "r".

  • vmin (float, optional) – The minimum value for the colormap. If None, will be set to minimum value in column_to_plot, by default None.

  • vmax (float, optional) – The maximum value for the colormap. If None, will be set to the maximum value in column_to_plot, by default None.

  • alpha (float, optional) – Transparency level for plotting value with floating point values ranging from 0.0 (transparent) to 1 (opaque), by default 1.0.

  • cmap (str, optional) – Color map used to visualize chosen column_to_plot values, by default "viridis".

  • discrete_cmap (int, optional) – Number of discrete colors to use in color map, by default 256.

  • plot_histogram (bool, optional) – If True, plot histograms of the value of images. By default False.

  • save_kml_dir (str or bool, optional) – If True, save KML files of the images. If a string is provided, it is the path to the directory in which to save the KML files. If set to False, no files are saved. By default False.

  • image_width_resolution (int or None, optional) –

    The pixel width to be used for plotting. If None, the resolution is not changed. Default is None.

    Note: Only relevant when tree_level="parent".

  • kml_dpi_image (int or None, optional) – The resolution, in dots per inch, to create KML images when save_kml_dir is specified (as either True or with path). By default None.

Returns:

A list of figures created by the method.

Return type:

list

load_patches(patch_paths, patch_file_ext=False, parent_paths=False, parent_file_ext=False, add_geo_info=False, clear_images=False)

Loads patch images from the given paths and adds them to the images dictionary in the MapImages instance.

Parameters:

  • patch_paths (str) –

    The file path of the patches to be loaded.

    Note: The ``patch_paths`` parameter accepts wildcards.

  • patch_file_ext (str or bool, optional) – The file extension of the patches to be loaded, ignored if file extensions are specified in patch_paths (e.g. with "./path/to/dir/*png") By default False.

  • parent_paths (str or bool, optional) –

    The file path of the parent images to be loaded. If set to False, no parents are loaded. Default is False.

    Note: The ``parent_paths`` parameter accepts wildcards.

  • parent_file_ext (str or bool, optional) – The file extension of the parent images, ignored if file extensions are specified in parent_paths (e.g. with "./path/to/dir/*png") By default False.

  • add_geo_info (bool, optional) – If True, adds geographic information to the parent image. Default is False.

  • clear_images (bool, optional) – If True, clears the images from the images dictionary before loading. Default is False.

Return type:

None

static detect_parent_id_from_path(image_id, parent_delimiter='#')

Detect parent IDs from image_id.

Parameters:

  • image_id (int or str) – ID of patch.

  • parent_delimiter (str, optional) – Delimiter used to separate parent ID when naming patch, by default "#".

Returns:

Parent ID.

Return type:

str

static detect_pixel_bounds_from_path(image_id)

Detects borders from the path assuming patch is named using the following format: ...-min_x-min_y-max_x-max_y-...

Parameters:

  • image_id (int or str) – ID of image

  • .. –

    border_delimiterstr, optional

    Delimiter used to separate border values when naming patch image, by default "-".

Returns:

Border (min_x, min_y, max_x, max_y) of image

Return type:

tuple of min_x, min_y, max_x, max_y

load_parents(parent_paths=False, parent_ids=False, parent_file_ext=False, overwrite=False, add_geo_info=False)

Load parent images from file paths (parent_paths).

If parent_paths is not given, only parent_ids, no image path will be added to the images.

Parameters:

  • parent_paths (str or bool, optional) – Path to parent images, by default False.

  • parent_ids (list, str or bool, optional) – ID(s) of parent images. Ignored if parent_paths are specified. By default False.

  • parent_file_ext (str or bool, optional) – The file extension of the parent images, ignored if file extensions are specified in parent_paths (e.g. with "./path/to/dir/*png") By default False.

  • overwrite (bool, optional) – If True, current parents will be overwritten, by default False.

  • add_geo_info (bool, optional) – If True, geographical info will be added to parents, by default False.

Return type:

None

load_df(parent_df=None, patch_df=None, clear_images=True)

Create MapImages instance by loading data from pandas DataFrame(s).

Parameters:

  • parent_df (pandas.DataFrame, optional) – DataFrame containing parents or path to parents, by default None.

  • patch_df (pandas.DataFrame, optional) – DataFrame containing patches, by default None.

  • clear_images (bool, optional) – If True, clear images before reading the dataframes, by default True.

Return type:

None

load_csv(parent_path=None, patch_path=None, clear_images=False, index_col_patch=0, index_col_parent=0, delimiter=',')

Load CSV files containing information about parent and patches, and update the images attribute of the MapImages instance with the loaded data.

Parameters:

  • parent_path (str, optional) – Path to the CSV file containing parent image information.

  • patch_path (str, optional) – Path to the CSV file containing patch information.

  • clear_images (bool, optional) – If True, clear all previously loaded image information before loading new information. Default is False.

  • index_col_patch (int, optional) – Column to set as index for the patch DataFrame, by default 0.

  • index_col_parent (int, optional) – Column to set as index for the parent DataFrame, by default 0.

  • delimiter (str, optional) – The delimiter to use when reading the dataframe. By default ",".

Return type:

None

add_geo_info(target_crs='EPSG:4326', verbose=True)

Add coordinates (reprojected to EPSG:4326) to all parents images using image metadata.

Parameters:

  • target_crs (str, optional) – Projection to convert coordinates into, by default "EPSG:4326".

  • verbose (bool, optional) – Whether to print verbose output, by default True

Return type:

None

Notes

For each image in the parents dictionary, this method calls _add_geo_info_id and coordinates (if present) to the image in the parent dictionary.

save_parents_as_geotiffs(rewrite=False, verbose=False, crs=None)

Save all parents in MapImages instance as geotiffs.

Parameters:

  • rewrite (bool, optional) – Whether to rewrite files if they already exist, by default False

  • verbose (bool, optional) – Whether to print verbose outputs, by default False

  • crs (str, optional) – The CRS of the coordinates. If None, the method will first look for crs in the parents dictionary and use those. If crs cannot be found in the dictionary, the method will use “EPSG:4326”. By default None.

Return type:

None

save_patches_as_geotiffs(rewrite=False, verbose=False, crs=None)

Save all patches in MapImages instance as geotiffs.

Parameters:

  • rewrite (bool, optional) – Whether to rewrite files if they already exist, by default False

  • verbose (bool, optional) – Whether to print verbose outputs, by default False

  • crs (str, optional) – The CRS of the coordinates. If None, the method will first look for crs in the patches dictionary and use those. If crs cannot be found in the dictionary, the method will use “EPSG:4326”. By default None.

Return type:

None

save_patches_to_geojson(geojson_fname='patches.geojson', rewrite=False, crs=None)

Saves patches to a geojson file.

Parameters:

  • geojson_fname (Optional[str], optional) – The name of the geojson file, by default “patches.geojson”

  • rewrite (Optional[bool], optional) – Whether to overwrite an existing file, by default False.

  • crs (Optional[str], optional) – The CRS to use when writing the geojson. If None, the method will look for “crs” in the patches dictionary and, if found, will use that. Otherwise it will set the crs to the default value of “EPSG:4326”. By default None

Return type:

None