pingmapper 5.5.0__tar.gz → 5.5.1__tar.gz

{pingmapper-5.5.0 → pingmapper-5.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.5.0
+Version: 5.5.1
 Summary: Open-source interface for processing recreation-grade side scan sonar datasets and reproducibly mapping benthic habitat
 Author: Cameron Bodine, Daniel Buscombe, Iury T Simoes-Sousa
 Author-email: bodine.cs@gmail.email

{pingmapper-5.5.0 → pingmapper-5.5.1}/pingmapper/class_mapSubstrateObj.py

@@ -880,7 +880,7 @@ class mapSubObj(rectObj):
             ax.imshow(son, cmap='gray')
 
             # Prepare color map
-            color_map = plt.cm.get_cmap('viridis')
+            color_map = plt.get_cmap('viridis')
 
             im = ax.imshow(c, cmap=color_map, alpha=0.5, vmin=minSoft, vmax=maxSoft)
             ax.axis('off')

{pingmapper-5.5.0 → pingmapper-5.5.1}/pingmapper/class_portstarObj.py

@@ -3185,7 +3185,11 @@ class portstarObj(object):
 
         for feature in dst_layer:
             subID = str(int(feature.GetField('Substrate')))
-            subName = MY_CLASS_NAMES[subID]
+            subName = MY_CLASS_NAMES.get(subID)
+            if subName is None:
+                print("\n\tWARNING: Unexpected substrate value '{}' found in raster. "
+                      "This value is not in the model config and will be removed from output.".format(subID))
+                subName = 'Unknown'
             feature.SetField('Name', subName)
             dst_layer.SetFeature(feature)
 
@@ -3204,10 +3208,12 @@ class portstarObj(object):
             feature.SetField("Area_m", area)
             dst_layer.SetFeature(feature)
 
-        # Delete NoData Polygon
+        # Delete NoData and any unexpected-value polygons
         # https://gis.stackexchange.com/questions/254444/deleting-selected-features-from-vector-ogr-in-gdal-python
+        valid_sub_ids = [int(k) for k in MY_CLASS_NAMES.keys() if int(k) != 0]
+        invalid_filter = "Substrate NOT IN ({})".format(','.join(str(v) for v in valid_sub_ids))
         layer = dst_ds.GetLayer()
-        layer.SetAttributeFilter("Substrate = 0")
+        layer.SetAttributeFilter(invalid_filter)
 
         for feat in layer:
             layer.DeleteFeature(feat.GetFID())

{pingmapper-5.5.0 → pingmapper-5.5.1}/pingmapper/class_rectObj.py

@@ -1968,7 +1968,7 @@ class rectObj(sonObj):
                     use_uint8_rgb = self._export_colormap_as_uint8()
                     if source_scale_bounds is not None:
                         norm_data = self._normalize_with_bounds(sonRect_raw16, source_scale_bounds[0], source_scale_bounds[1])
-                        cmap = plt.cm.get_cmap(self.son_colorMap_name)(norm_data)
+                        cmap = plt.get_cmap(self.son_colorMap_name)(norm_data)
                         if use_uint8_rgb:
                             sonRect_out = np.clip(cmap[:, :, :3] * 255.0, 0, 255).astype(np.uint8)
                         else:
@@ -2769,9 +2769,9 @@ class rectObj(sonObj):
                     if source_scale_bounds is not None:
                         norm_data = self._normalize_with_bounds(out16_raw, source_scale_bounds[0], source_scale_bounds[1])
                         if use_uint8_rgb:
-                            out16 = np.clip(plt.cm.get_cmap(self.son_colorMap_name)(norm_data)[:, :, :3] * 255.0, 0, 255).astype(np.uint8)
+                            out16 = np.clip(plt.get_cmap(self.son_colorMap_name)(norm_data)[:, :, :3] * 255.0, 0, 255).astype(np.uint8)
                         else:
-                            out16 = np.clip(plt.cm.get_cmap(self.son_colorMap_name)(norm_data)[:, :, :3] * 65535.0, 0, 65535).astype(np.uint16)
+                            out16 = np.clip(plt.get_cmap(self.son_colorMap_name)(norm_data)[:, :, :3] * 65535.0, 0, 65535).astype(np.uint16)
                         valid_mask = out16_raw > 0
                         out16[valid_mask] = np.maximum(out16[valid_mask], 1)
                     else:
@@ -2914,9 +2914,9 @@ class rectObj(sonObj):
                     if source_scale_bounds is not None:
                         norm_data = self._normalize_with_bounds(out16_raw, source_scale_bounds[0], source_scale_bounds[1])
                         if use_uint8_rgb:
-                            out16 = np.clip(plt.cm.get_cmap(self.son_colorMap_name)(norm_data)[:, :, :3] * 255.0, 0, 255).astype(np.uint8)
+                            out16 = np.clip(plt.get_cmap(self.son_colorMap_name)(norm_data)[:, :, :3] * 255.0, 0, 255).astype(np.uint8)
                         else:
-                            out16 = np.clip(plt.cm.get_cmap(self.son_colorMap_name)(norm_data)[:, :, :3] * 65535.0, 0, 65535).astype(np.uint16)
+                            out16 = np.clip(plt.get_cmap(self.son_colorMap_name)(norm_data)[:, :, :3] * 65535.0, 0, 65535).astype(np.uint16)
                         valid_mask = out16_raw > 0
                         out16[valid_mask] = np.maximum(out16[valid_mask], 1)
                     else:

{pingmapper-5.5.0 → pingmapper-5.5.1}/pingmapper/class_sonObj.py

@@ -1872,7 +1872,7 @@ class sonObj(object):
         return out
 
     def _colorize_array_batched(self, norm_data, valid_mask, cmap_name, scale_max, out_dtype):
-        cmap = plt.cm.get_cmap(cmap_name)
+        cmap = plt.get_cmap(cmap_name)
         height, width = norm_data.shape
         out = np.zeros((height, width, 3), dtype=out_dtype)
 

{pingmapper-5.5.0 → pingmapper-5.5.1}/pingmapper/class_sonObj_nadirgaptest.py

@@ -1500,7 +1500,7 @@ class sonObj(object):
             # plt.savefig(outfile)
 
             norm_data = data / 255.0
-            colored_data = plt.cm.get_cmap(self.sonogram_colorMap)(norm_data)
+            colored_data = plt.get_cmap(self.sonogram_colorMap)(norm_data)
             colored_data = (colored_data[:, :, :3] * 255).astype('uint8')
             data = colored_data
 

pingmapper-5.5.1/pingmapper/version.py

@@ -0,0 +1 @@
+__version__ = '5.5.1'

{pingmapper-5.5.0 → pingmapper-5.5.1}/pingmapper.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.5.0
+Version: 5.5.1
 Summary: Open-source interface for processing recreation-grade side scan sonar datasets and reproducibly mapping benthic habitat
 Author: Cameron Bodine, Daniel Buscombe, Iury T Simoes-Sousa
 Author-email: bodine.cs@gmail.email

pingmapper-5.5.0/pingmapper/version.py

@@ -1 +0,0 @@
-__version__ = '5.5.0'