megadetector 5.0.28__py3-none-any.whl → 10.0.0__py3-none-any.whl

megadetector/utils/write_html_image_list.py

@@ -23,25 +23,25 @@ from megadetector.utils import path_utils
 
 def write_html_image_list(filename=None,images=None,options=None):
     """
-    Given a list of image file names, writes an HTML file that shows all those images, 
+    Given a list of image file names, writes an HTML file that shows all those images,
     with optional one-line headers above each.
 
     Args:
-        filename (str, optional): the .html output file; if None, just returns a valid 
+        filename (str, optional): the .html output file; if None, just returns a valid
             options dict
-        images (list, optional): the images to write to the .html file; if None, just returns 
+        images (list, optional): the images to write to the .html file; if None, just returns
             a valid options dict.  This can be a flat list of image filenames, or this can
             be a list of dictionaries with one or more of the following fields:
-                
+
             - filename (image filename) (required, all other fields are optional)
             - imageStyle (css style for this image)
             - textStyle (css style for the title associated with this image)
             - title (text label for this image)
             - linkTarget (URL to which this image should link on click)
-            
-        options (dict, optional): a dict with one or more of the following fields:        
-            
-            - fHtml (file pointer to write to, used for splitting write operations over multiple calls)
+
+        options (dict, optional): a dict with one or more of the following fields:
+
+            - f_html (file pointer to write to, used for splitting write operations over multiple calls)
             - pageTitle (HTML page title)
             - headerHtml (html text to include before the image list)
             - subPageHeaderHtml (html text to include before the images when images are broken into pages)
@@ -52,28 +52,28 @@ def write_html_image_list(filename=None,images=None,options=None):
               multiple files and a TOC with links)
             - urlEncodeFilenames (default True, e.g. '#' will be replaced by '%23')
             - urlEncodeLinkTargets (default True, e.g. '#' will be replaced by '%23')
-            
+
     """
-    
+
     # returns an options struct
     if options is None:
         options = {}
-        
-    if 'fHtml' not in options:
-        options['fHtml'] = -1
-    
+
+    if 'f_html' not in options:
+        options['f_html'] = -1
+
     if 'pageTitle' not in options or options['pageTitle'] is None:
         options['pageTitle'] = ''
-        
+
     if 'headerHtml' not in options or options['headerHtml'] is None:
         options['headerHtml'] = ''
-    
+
     if 'subPageHeaderHtml' not in options or options['subPageHeaderHtml'] is None:
         options['subPageHeaderHtml'] = ''
-        
+
     if 'trailerHtml' not in options or options['trailerHtml'] is None:
         options['trailerHtml'] = ''
-    
+
     if 'defaultTextStyle' not in options or options['defaultTextStyle'] is None:
         options['defaultTextStyle'] = \
         "font-family:calibri,verdana,arial;font-weight:bold;font-size:150%;text-align:left;margin:0px;"
@@ -81,160 +81,160 @@ def write_html_image_list(filename=None,images=None,options=None):
     if 'defaultImageStyle' not in options or options['defaultImageStyle'] is None:
         options['defaultImageStyle'] = \
         "margin:0px;margin-top:5px;margin-bottom:5px;"
-    
+
     if 'urlEncodeFilenames' not in options or options['urlEncodeFilenames'] is None:
         options['urlEncodeFilenames'] = True
-    
+
     if 'urlEncodeLinkTargets' not in options or options['urlEncodeLinkTargets'] is None:
         options['urlEncodeLinkTargets'] = True
-    
+
     # Possibly split the html output for figures into multiple files; Chrome gets sad with
-    # thousands of images in a single tab.        
+    # thousands of images in a single tab.
     if 'maxFiguresPerHtmlFile' not in options or options['maxFiguresPerHtmlFile'] is None:
-        options['maxFiguresPerHtmlFile'] = math.inf    
-    
+        options['maxFiguresPerHtmlFile'] = math.inf
+
     if filename is None or images is None:
         return options
-    
-    # images may be a list of images or a list of image/style/title dictionaries, 
+
+    # images may be a list of images or a list of image/style/title dictionaries,
     # enforce that it's the latter to simplify downstream code
-    for iImage,imageInfo in enumerate(images):
-        if isinstance(imageInfo,str):
-            imageInfo = {'filename':imageInfo}
-        if 'filename' not in imageInfo:
-            imageInfo['filename'] = ''
-        if 'imageStyle' not in imageInfo:
-            imageInfo['imageStyle'] = options['defaultImageStyle']
-        if 'title' not in imageInfo:
-            imageInfo['title'] = ''
-        if 'linkTarget' not in imageInfo:
-            imageInfo['linkTarget'] = ''
-        if 'textStyle' not in imageInfo:
-            textStyle = options['defaultTextStyle']
-            imageInfo['textStyle'] = options['defaultTextStyle']
-        images[iImage] = imageInfo            
-    
-    nImages = len(images)
-    
+    for i_image,image_info in enumerate(images):
+        if isinstance(image_info,str):
+            image_info = {'filename':image_info}
+        if 'filename' not in image_info:
+            image_info['filename'] = ''
+        if 'imageStyle' not in image_info:
+            image_info['imageStyle'] = options['defaultImageStyle']
+        if 'title' not in image_info:
+            image_info['title'] = ''
+        if 'linkTarget' not in image_info:
+            image_info['linkTarget'] = ''
+        if 'textStyle' not in image_info:
+            text_style = options['defaultTextStyle']
+            image_info['textStyle'] = options['defaultTextStyle']
+        images[i_image] = image_info
+
+    n_images = len(images)
+
     # If we need to break this up into multiple files...
-    if nImages > options['maxFiguresPerHtmlFile']:
-    
+    if n_images > options['maxFiguresPerHtmlFile']:
+
         # You can't supply your own file handle in this case
-        if options['fHtml'] != -1:
+        if options['f_html'] != -1:
             raise ValueError(
                     "You can't supply your own file handle if we have to page the image set")
-        
-        figureFileStartingIndices = list(range(0,nImages,options['maxFiguresPerHtmlFile']))
 
-        assert len(figureFileStartingIndices) > 1
-        
+        figure_file_starting_indices = list(range(0,n_images,options['maxFiguresPerHtmlFile']))
+
+        assert len(figure_file_starting_indices) > 1
+
         # Open the meta-output file
-        fMeta = open(filename,'w')
-        
+        f_meta = open(filename,'w')
+
         # Write header stuff
-        titleString = '<title>Index page</title>'
+        title_string = '<title>Index page</title>'
         if len(options['pageTitle']) > 0:
-            titleString = '<title>Index page for: {}</title>'.format(options['pageTitle'])
-        fMeta.write('<html><head>{}</head><body>\n'.format(titleString))
-        fMeta.write(options['headerHtml'])        
-        fMeta.write('<table border = 0 cellpadding = 2>\n')
-        
-        for startingIndex in figureFileStartingIndices:
-            
-            iStart = startingIndex
-            iEnd = startingIndex+options['maxFiguresPerHtmlFile']-1;
-            if iEnd >= nImages:
-                iEnd = nImages-1
-            
-            trailer = 'image_{:05d}_{:05d}'.format(iStart,iEnd)
-            localFiguresHtmlFilename = path_utils.insert_before_extension(filename,trailer)
-            fMeta.write('<tr><td>\n')
-            fMeta.write('<p style="padding-bottom:0px;margin-bottom:0px;text-align:left;font-family:''segoe ui'',calibri,arial;font-size:100%;text-decoration:none;font-weight:bold;">')
-            fMeta.write('<a href="{}">Figures for images {} through {}</a></p></td></tr>\n'.format(
-                os.path.basename(localFiguresHtmlFilename),iStart,iEnd))
-            
-            localImages = images[iStart:iEnd+1]
-            
-            localOptions = options.copy();
-            localOptions['headerHtml'] = options['subPageHeaderHtml'];
-            localOptions['trailerHtml'] = '';
-            
+            title_string = '<title>Index page for: {}</title>'.format(options['pageTitle'])
+        f_meta.write('<html><head>{}</head><body>\n'.format(title_string))
+        f_meta.write(options['headerHtml'])
+        f_meta.write('<table border = 0 cellpadding = 2>\n')
+
+        for starting_index in figure_file_starting_indices:
+
+            i_start = starting_index
+            i_end = starting_index + options['maxFiguresPerHtmlFile'] - 1
+            if i_end >= n_images:
+                i_end = n_images-1
+
+            trailer = 'image_{:05d}_{:05d}'.format(i_start,i_end)
+            local_figures_html_filename = path_utils.insert_before_extension(filename,trailer)
+            f_meta.write('<tr><td>\n')
+            f_meta.write('<p style="padding-bottom:0px;margin-bottom:0px;text-align:left;font-family:''segoe ui'',calibri,arial;font-size:100%;text-decoration:none;font-weight:bold;">') # noqa
+            f_meta.write('<a href="{}">Figures for images {} through {}</a></p></td></tr>\n'.format(
+                os.path.basename(local_figures_html_filename),i_start,i_end))
+
+            local_images = images[i_start:i_end+1]
+
+            local_options = options.copy()
+            local_options['headerHtml'] = options['subPageHeaderHtml']
+            local_options['trailerHtml'] = ''
+
             # Make a recursive call for this image set
-            write_html_image_list(localFiguresHtmlFilename,localImages,localOptions)
-            
+            write_html_image_list(local_figures_html_filename,local_images,local_options)
+
         # ...for each page of images
-        
-        fMeta.write('</table></body>\n')
-        fMeta.write(options['trailerHtml'])
-        fMeta.write('</html>\n')
-        fMeta.close()
-        
+
+        f_meta.write('</table></body>\n')
+        f_meta.write(options['trailerHtml'])
+        f_meta.write('</html>\n')
+        f_meta.close()
+
         return options
-        
+
     # ...if we have to make multiple sub-pages
-        
-    bCleanupFile = False
-    
-    if options['fHtml'] == -1:
-        bCleanupFile = True;
-        fHtml = open(filename,'w')
+
+    b_clean_up_file = False
+
+    if options['f_html'] == -1:
+        b_clean_up_file = True
+        f_html = open(filename,'w')
     else:
-        fHtml = options['fHtml']
-        
-    titleString = ''
+        f_html = options['f_html']
+
+    title_string = ''
     if len(options['pageTitle']) > 0:
-        titleString = '<title>{}</title>'.format(options['pageTitle'])
-    
-    fHtml.write('<html>{}<body>\n'.format(titleString))
-    
-    fHtml.write(options['headerHtml'])
-    
+        title_string = '<title>{}</title>'.format(options['pageTitle'])
+
+    f_html.write('<html>{}<body>\n'.format(title_string))
+
+    f_html.write(options['headerHtml'])
+
     # Write out images
-    for iImage,image in enumerate(images):
-        
+    for i_image,image in enumerate(images):
+
         title = image['title']
-        imageStyle = image['imageStyle']
-        textStyle = image['textStyle']
+        image_style = image['imageStyle']
+        text_style = image['textStyle']
         filename = image['filename']
-        linkTarget = image['linkTarget']
-        
+        link_target = image['linkTarget']
+
         # Remove unicode characters
         title = title.encode('ascii','ignore').decode('ascii')
         filename = filename.encode('ascii','ignore').decode('ascii')
-        
+
         filename = filename.replace('\\','/')
-        if options['urlEncodeFilenames']:            
+        if options['urlEncodeFilenames']:
             filename = urllib.parse.quote(filename)
-        
-        if len(title) > 0:       
-            fHtml.write(
+
+        if len(title) > 0:
+            f_html.write(
                     '<p style="{}">{}</p>\n'\
-                    .format(textStyle,title))            
+                    .format(text_style,title))
 
-        linkTarget = linkTarget.replace('\\','/')
+        link_target = link_target.replace('\\','/')
         if options['urlEncodeLinkTargets']:
             # These are typically absolute paths, so we only want to mess with certain characters
-            linkTarget = urllib.parse.quote(linkTarget,safe=':/')
-            
-        if len(linkTarget) > 0:
-            fHtml.write('<a href="{}">'.format(linkTarget))
-            # imageStyle.append(';border:0px;')
-        
-        fHtml.write('<img src="{}" style="{}">\n'.format(filename,imageStyle))
-        
-        if len(linkTarget) > 0:
-            fHtml.write('</a>')
-            
-        if iImage != len(images)-1:
-            fHtml.write('<br/>')             
-            
+            link_target = urllib.parse.quote(link_target,safe=':/')
+
+        if len(link_target) > 0:
+            f_html.write('<a href="{}">'.format(link_target))
+            # image_style.append(';border:0px;')
+
+        f_html.write('<img src="{}" style="{}">\n'.format(filename,image_style))
+
+        if len(link_target) > 0:
+            f_html.write('</a>')
+
+        if i_image != len(images)-1:
+            f_html.write('<br/>')
+
     # ...for each image we need to write
-    
-    fHtml.write(options['trailerHtml'])
-    
-    fHtml.write('</body></html>\n')
-    
-    if bCleanupFile:
-        fHtml.close()    
+
+    f_html.write(options['trailerHtml'])
+
+    f_html.write('</body></html>\n')
+
+    if b_clean_up_file:
+        f_html.close()
 
 # ...function

megadetector/visualization/plot_utils.py

@@ -34,22 +34,22 @@ def plot_confusion_matrix(matrix,
         matrix (np.ndarray): shape [num_classes, num_classes], confusion matrix
             where rows are ground-truth classes and columns are predicted classes
         classes (list of str): class names for each row/column
-        normalize (bool, optional): whether to perform row-wise normalization; 
+        normalize (bool, optional): whether to perform row-wise normalization;
             by default, assumes values in the confusion matrix are percentages
         title (str, optional): figure title
-        cmap (matplotlib.colors.colormap): colormap for cell backgrounds
-        vmax (float, optional), value corresponding to the largest value of the colormap;
+        cmap (matplotlib.colors.colormap, optional): colormap for cell backgrounds
+        vmax (float, optional): value corresponding to the largest value of the colormap;
             if None, the maximum value in [matrix] will be used
         use_colorbar (bool, optional): whether to show colorbar
         y_label (bool, optional): whether to show class names on the y axis
-        fmt (str): format string for rendering numeric values
-        fig (Figure): existing figure to which we should render, otherwise creates
-            a new figure
-        
-    Returns: 
+        fmt (str, optional): format string for rendering numeric values
+        fig (Figure, optional): existing figure to which we should render, otherwise
+            creates a new figure
+
+    Returns:
         matplotlib.figure.Figure: the figure we rendered to or created
     """
-    
+
     num_classes = matrix.shape[0]
     assert matrix.shape[1] == num_classes
     assert len(classes) == num_classes
@@ -86,7 +86,7 @@ def plot_confusion_matrix(matrix,
         ax.set_ylabel('Ground-truth class')
 
     for i, j in np.ndindex(matrix.shape):
-        v = matrix[i, j]        
+        v = matrix[i, j]
         ax.text(j, i, fmt.format(v),
                 horizontalalignment='center',
                 verticalalignment='center',
@@ -97,8 +97,8 @@ def plot_confusion_matrix(matrix,
 # ...def plot_confusion_matrix(...)
 
 
-def plot_precision_recall_curve(precisions, 
-                                recalls, 
+def plot_precision_recall_curve(precisions,
+                                recalls,
                                 title='Precision/recall curve',
                                 xlim=(0.0,1.05),
                                 ylim=(0.0,1.05)):
@@ -115,10 +115,10 @@ def plot_precision_recall_curve(precisions,
         xlim (tuple, optional): x-axis limits as a length-2 tuple
         ylim (tuple, optional): y-axis limits as a length-2 tuple
 
-    Returns: 
+    Returns:
         matplotlib.figure.Figure: the (new) figure
     """
-    
+
     assert len(precisions) == len(recalls)
 
     fig = matplotlib.figure.Figure(tight_layout=True)
@@ -128,23 +128,27 @@ def plot_precision_recall_curve(precisions,
 
     try:
         ax.set(x_label='Recall', y_label='Precision', title=title)
-        ax.set(x_lim=xlim, y_lim=ylim)    
-    # 
+        ax.set(x_lim=xlim, y_lim=ylim)
+    #
     except Exception:
         ax.set_xlabel('Recall')
         ax.set_ylabel('Precision')
         ax.set_title(title)
         ax.set_xlim(xlim[0],xlim[1])
         ax.set_ylim(ylim[0],ylim[1])
-        
+
     return fig
 
 
-def plot_stacked_bar_chart(data, series_labels=None, col_labels=None,
-                           x_label=None, y_label=None, log_scale=False):
+def plot_stacked_bar_chart(data,
+                           series_labels=None,
+                           col_labels=None,
+                           x_label=None,
+                           y_label=None,
+                           log_scale=False):
     """
     Plot a stacked bar chart, for plotting e.g. species distribution across locations.
-    
+
     Reference: https://stackoverflow.com/q/44309507
 
     Args:
@@ -154,12 +158,12 @@ def plot_stacked_bar_chart(data, series_labels=None, col_labels=None,
         col_labels (list of str, optional): column labels, typically location names
         x_label (str, optional): x-axis label
         y_label (str, optional): y-axis label
-        log_scale (bool, optional) whether to plot the y axis in log-scale
+        log_scale (bool, optional): whether to plot the y axis in log-scale
 
-    Returns: 
+    Returns:
         matplotlib.figure.Figure: the (new) figure
     """
-    
+
     data = np.asarray(data)
     num_series, num_columns = data.shape
     ind = np.arange(num_columns)
@@ -206,24 +210,24 @@ def calibration_ece(true_scores, pred_scores, num_bins):
 
     Implementation modified from sklearn.calibration.calibration_curve()
     in order to implement ECE calculation. See:
-    
+
     https://github.com/scikit-learn/scikit-learn/issues/18268
 
     Args:
         true_scores (list of int): true values, length N, binary-valued (0 = neg, 1 = pos)
-        pred_scores (list of float): predicted confidence values, length N, pred_scores[i] is the 
+        pred_scores (list of float): predicted confidence values, length N, pred_scores[i] is the
             predicted confidence that example i is positive
         num_bins (int): number of bins to use (`M` in eq. (3) of Guo 2017)
 
     Returns:
         tuple: a length-three tuple containing:
             - accs: np.ndarray, shape [M], type float64, accuracy in each bin,
-              M <= num_bins because bins with no samples are not returned        
+              M <= num_bins because bins with no samples are not returned
             - confs: np.ndarray, shape [M], type float64, mean model confidence in
               each bin
             - ece: float, expected calibration error
     """
-    
+
     assert len(true_scores) == len(pred_scores)
 
     bins = np.linspace(0., 1. + 1e-8, num=num_bins + 1)
@@ -250,19 +254,19 @@ def plot_calibration_curve(true_scores, pred_scores, num_bins,
 
     Args:
         true_scores (list of int): true values, length N, binary-valued (0 = neg, 1 = pos)
-        pred_scores (list of float): predicted confidence values, length N, pred_scores[i] is the 
+        pred_scores (list of float): predicted confidence values, length N, pred_scores[i] is the
             predicted confidence that example i is positive
         num_bins (int): number of bins to use (`M` in eq. (3) of Guo 2017)
         name (str, optional): label in legend for the calibration curve
         plot_perf (bool, optional): whether to plot y=x line indicating perfect calibration
         plot_hist (bool, optional): whether to plot histogram of counts
         ax (Axes, optional): if given then no legend is drawn, and fig_kwargs are ignored
-        fig_kwargs (dict, optional): only used if [ax] is None
+        fig_kwargs (dict): only used if [ax] is None
 
     Returns:
         matplotlib.figure.Figure: the (new) figure
     """
-    
+
     accs, confs, ece = calibration_ece(true_scores, pred_scores, num_bins)
 
     created_fig = False