pingmapper 5.5.2__tar.gz → 5.5.3__tar.gz

{pingmapper-5.5.2 → pingmapper-5.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.5.2
+Version: 5.5.3
 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-5.5.2 → pingmapper-5.5.3}/pingmapper/class_rectObj.py

@@ -2724,6 +2724,8 @@ class rectObj(sonObj):
             img = self.sonDat.copy()
             if son:
                 img = self._reserve_zero_for_nodata(img, preserve_zeros=True)
+                if bool(getattr(self, 'sonar_db_transform', False)) or bool(getattr(self, 'sonar_clahe', False)):
+                    img = self._apply_display_enhancements(img)
             apply_post_rect_colormap = use_16bit and self._rect_colormap_selected(son=son)
             source_scale_bounds = None
             if apply_post_rect_colormap:
@@ -2747,6 +2749,8 @@ class rectObj(sonObj):
             out = np.flip(np.flip(np.flip(out,1),0),1)
             if use_16bit:
                 out = out.astype(np.float32)
+            elif bool(getattr(self, 'sonar_db_transform', False)) or bool(getattr(self, 'sonar_clahe', False)):
+                out = out.astype(np.float32)
             else:
                 out = out.astype('uint8')
 
@@ -2780,7 +2784,10 @@ class rectObj(sonObj):
                     out16 = out16_raw
                 self._write_rect_geotiff(gtiff, out16, epsg, transform, colormap=None)
             else:
-                out8 = np.clip(out, 0, 255).astype(np.uint8)
+                if bool(getattr(self, 'sonar_db_transform', False)) or bool(getattr(self, 'sonar_clahe', False)):
+                    out8 = self._convert_son_dat_to_uint8(out)
+                else:
+                    out8 = np.clip(out, 0, 255).astype(np.uint8)
                 self._write_rect_geotiff(gtiff, out8, epsg, transform, colormap=self.son_colorMap)
 
             del out, img
@@ -2815,6 +2822,8 @@ class rectObj(sonObj):
             img = self.sonDat
             if son:
                 img = self._reserve_zero_for_nodata(img, preserve_zeros=True)
+                if bool(getattr(self, 'sonar_db_transform', False)) or bool(getattr(self, 'sonar_clahe', False)):
+                    img = self._apply_display_enhancements(img)
             apply_post_rect_colormap = son and use_16bit and self._rect_colormap_selected(son=son)
             source_scale_bounds = None
             if apply_post_rect_colormap:
@@ -2887,6 +2896,8 @@ class rectObj(sonObj):
             out = np.flip(np.flip(np.flip(out,1),0),1)
             if son and use_16bit:
                 out = out.astype(np.float32)
+            elif son and (bool(getattr(self, 'sonar_db_transform', False)) or bool(getattr(self, 'sonar_clahe', False))):
+                out = out.astype(np.float32)
             else:
                 out = out.astype('uint8')
 
@@ -2926,7 +2937,10 @@ class rectObj(sonObj):
                 self._write_rect_geotiff(gtiff, out16, epsg, transform, colormap=None)
             else:
                 colormap = self.son_colorMap if son else class_colormap
-                out8 = np.clip(out, 0, 255).astype(np.uint8)
+                if son and (bool(getattr(self, 'sonar_db_transform', False)) or bool(getattr(self, 'sonar_clahe', False))):
+                    out8 = self._convert_son_dat_to_uint8(out)
+                else:
+                    out8 = np.clip(out, 0, 255).astype(np.uint8)
                 self._write_rect_geotiff(gtiff, out8, epsg, transform, colormap=colormap)
 
             del out

{pingmapper-5.5.2 → pingmapper-5.5.3}/pingmapper/class_sonObj.py

@@ -1319,6 +1319,44 @@ class sonObj(object):
         if not use_db and not use_clahe:
             return sonDat
 
+        arr = self._apply_display_db_transform(sonDat)
+        if arr.size == 0:
+            return arr
+
+        valid = arr > 0
+        if not np.any(valid):
+            return arr
+
+        if use_clahe:
+            clip_limit = float(getattr(self, 'sonar_clahe_clip_limit', 0.01))
+            if (not np.isfinite(clip_limit)) or clip_limit <= 0:
+                clip_limit = 0.01
+
+            global_bounds = None
+            if bool(getattr(self, 'sonar_clahe_global', True)):
+                global_bounds = self._ensure_clahe_global_bounds()
+
+            if global_bounds is not None:
+                arr01 = self._normalize_with_bounds(arr, global_bounds[0], global_bounds[1])
+            else:
+                max_val = float(np.nanmax(arr))
+                if not (np.isfinite(max_val) and max_val > 0):
+                    return arr
+                arr01 = np.clip(arr / max_val, 0.0, 1.0)
+
+            try:
+                arr01 = exposure.equalize_adapthist(arr01, clip_limit=clip_limit)
+                arr = np.asarray(arr01, dtype=np.float32) * 255.0
+            except MemoryError:
+                arr = self._apply_clahe_chunked(arr01, clip_limit)
+            except np.core._exceptions._ArrayMemoryError:
+                arr = self._apply_clahe_chunked(arr01, clip_limit)
+
+        # Preserve no-data convention for empty samples.
+        arr[~valid] = 0.0
+        return arr
+
+    def _apply_display_db_transform(self, sonDat):
         arr = np.asarray(sonDat, dtype=np.float32)
         if arr.size == 0:
             return arr
@@ -1330,7 +1368,7 @@ class sonObj(object):
         if not np.any(valid):
             return arr
 
-        if use_db:
+        if bool(getattr(self, 'sonar_db_transform', False)):
             # Use the smallest positive intensity as the log floor to avoid
             # collapsing zeros to -inf and to preserve relative low amplitudes.
             floor = float(np.nanmin(arr[valid]))
@@ -1340,25 +1378,73 @@ class sonObj(object):
             arr = 20.0 * np.log10(arr)
             arr = arr - np.nanmin(arr)
 
-        if use_clahe:
-            max_val = float(np.nanmax(arr))
-            if np.isfinite(max_val) and max_val > 0:
-                arr01 = np.clip(arr / max_val, 0.0, 1.0)
-                clip_limit = float(getattr(self, 'sonar_clahe_clip_limit', 0.01))
-                if (not np.isfinite(clip_limit)) or clip_limit <= 0:
-                    clip_limit = 0.01
-                try:
-                    arr01 = exposure.equalize_adapthist(arr01, clip_limit=clip_limit)
-                    arr = np.asarray(arr01, dtype=np.float32)
-                except MemoryError:
-                    arr = self._apply_clahe_chunked(arr01, clip_limit)
-                except np.core._exceptions._ArrayMemoryError:
-                    arr = self._apply_clahe_chunked(arr01, clip_limit)
-
-        # Preserve no-data convention for empty samples.
         arr[~valid] = 0.0
         return arr
 
+    def _ensure_clahe_global_bounds(self):
+        if not bool(getattr(self, 'sonar_clahe_global', True)):
+            return None
+
+        cache = getattr(self, '_sonar_clahe_global_bounds', None)
+        if isinstance(cache, tuple) and len(cache) == 2:
+            lo, hi = cache
+            if np.isfinite(lo) and np.isfinite(hi) and hi > lo:
+                return cache
+
+        if not hasattr(self, 'sonMetaDF'):
+            self._loadSonMeta()
+
+        if not hasattr(self, 'sonMetaDF') or self.sonMetaDF is None or len(self.sonMetaDF) == 0:
+            return None
+
+        saved_sonDat = getattr(self, 'sonDat', None)
+        saved_sonDat16 = getattr(self, 'sonDat16', None)
+        saved_pingMax = getattr(self, 'pingMax', None)
+
+        chunk_ids = pd.unique(self.sonMetaDF['chunk_id'])
+        sample_cap = int(getattr(self, 'sonar_clahe_global_sample_cap', 200000))
+        if sample_cap <= 0:
+            sample_cap = 200000
+
+        sampled_vals = []
+        for chunk in chunk_ids:
+            self._getScanChunkSingle(int(chunk))
+            arr = self._apply_display_db_transform(self.sonDat)
+            valid = arr > 0
+            if not np.any(valid):
+                continue
+
+            vals = arr[valid].astype(np.float32, copy=False)
+            if vals.size > sample_cap:
+                idx = np.linspace(0, vals.size - 1, sample_cap, dtype=np.int64)
+                vals = vals[idx]
+            sampled_vals.append(vals)
+
+        if len(sampled_vals) == 0:
+            self.sonDat = saved_sonDat
+            self.sonDat16 = saved_sonDat16
+            self.pingMax = saved_pingMax
+            return None
+
+        pooled = np.concatenate(sampled_vals)
+        lo = float(np.nanpercentile(pooled, 1.0))
+        hi = float(np.nanpercentile(pooled, 99.5))
+        if (not np.isfinite(lo)) or (not np.isfinite(hi)) or hi <= lo:
+            lo = float(np.nanmin(pooled))
+            hi = float(np.nanmax(pooled))
+
+        if (not np.isfinite(lo)) or (not np.isfinite(hi)) or hi <= lo:
+            self.sonDat = saved_sonDat
+            self.sonDat16 = saved_sonDat16
+            self.pingMax = saved_pingMax
+            return None
+
+        self._sonar_clahe_global_bounds = (lo, hi)
+        self.sonDat = saved_sonDat
+        self.sonDat16 = saved_sonDat16
+        self.pingMax = saved_pingMax
+        return self._sonar_clahe_global_bounds
+
     def _apply_clahe_chunked(self, arr01, clip_limit):
         """Apply CLAHE in row-wise stripes to reduce peak memory usage."""
         src = np.asarray(arr01, dtype=np.float32)
@@ -1378,7 +1464,7 @@ class sonObj(object):
             end = min(start + stripe_rows, h)
             stripe = src[start:end, :]
             stripe_eq = exposure.equalize_adapthist(stripe, clip_limit=clip_limit)
-            out[start:end, :] = np.asarray(stripe_eq, dtype=np.float32)
+            out[start:end, :] = np.asarray(stripe_eq, dtype=np.float32) * 255.0
 
         return out
 

{pingmapper-5.5.2 → pingmapper-5.5.3}/pingmapper/default_params.json

@@ -27,6 +27,7 @@
     "tone_gain":1.0,
     "sonar_db_transform":false,
     "sonar_clahe":false,
+    "sonar_clahe_global":true,
     "sonar_clahe_clip_limit":0.01,
     "wcp":false,
     "wcm":true,

{pingmapper-5.5.2 → pingmapper-5.5.3}/pingmapper/gui_main.py

@@ -321,6 +321,12 @@ def gui(batch: bool):
         default=default_params.get('sonar_clahe', False),
         tooltip=tip_clahe,
     )
+    check_sonar_clahe_global = sg.Checkbox(
+        'Global CLAHE reference',
+        key='sonar_clahe_global',
+        default=default_params.get('sonar_clahe_global', True),
+        tooltip='Use one project-wide intensity reference before CLAHE so chunk brightness stays consistent. This adds a prepass, but reduces chunk-to-chunk contrast shifts.',
+    )
     text_clahe_clip = sg.Text('CLAHE Clip Limit', size=(20,1))
     in_clahe_clip = sg.Input(
         key='sonar_clahe_clip_limit',
@@ -335,6 +341,7 @@ def gui(batch: bool):
             [text_egn_gain, slide_egn_gain],
             [check_sonar_db],
             [check_sonar_clahe],
+            [check_sonar_clahe_global],
             [text_clahe_clip, in_clahe_clip],
         ],
         pad=0,
@@ -837,6 +844,7 @@ def gui(batch: bool):
             'tone_gain':float(values['tone_gain']),
             'sonar_db_transform':values['sonar_db_transform'],
             'sonar_clahe':values['sonar_clahe'],
+            'sonar_clahe_global':values['sonar_clahe_global'],
             'sonar_clahe_clip_limit':float(values['sonar_clahe_clip_limit']),
             'wcp':values['wcp'],
             'wcm':values['wcm'],

{pingmapper-5.5.2 → pingmapper-5.5.3}/pingmapper/main_readFiles.py

@@ -720,6 +720,7 @@ def read_master_func(logfilename='',
                      tone_gain=1.0,
                      sonar_db_transform=False,
                      sonar_clahe=False,
+                     sonar_clahe_global=True,
                      sonar_clahe_clip_limit=0.01,
                      wcp=False,
                      wcm=False,
@@ -1209,7 +1210,10 @@ def read_master_func(logfilename='',
             son.tone_gain = tone_gain
             son.sonar_db_transform = bool(sonar_db_transform)
             son.sonar_clahe = bool(sonar_clahe)
+            son.sonar_clahe_global = bool(sonar_clahe_global)
             son.sonar_clahe_clip_limit = float(sonar_clahe_clip_limit)
+            if son.sonar_clahe:
+                son._ensure_clahe_global_bounds()
             # Do range crop, if necessary
             if cropRange > 0.0:
                 if file_type == '.xtf' and _is_sidescan_beam(getattr(son, 'beamName', '')):
@@ -1405,7 +1409,10 @@ def read_master_func(logfilename='',
             son.tone_gain = tone_gain
             son.sonar_db_transform = bool(sonar_db_transform)
             son.sonar_clahe = bool(sonar_clahe)
+            son.sonar_clahe_global = bool(sonar_clahe_global)
             son.sonar_clahe_clip_limit = float(sonar_clahe_clip_limit)
+            if son.sonar_clahe:
+                son._ensure_clahe_global_bounds()
 
             beam = son.beamName
             if wcr:

{pingmapper-5.5.2 → pingmapper-5.5.3}/pingmapper/main_rectify.py

@@ -126,6 +126,10 @@ def rectify_master_func(logfilename='',
                         egn_stretch_factor=1,
                         tone_gamma=1.0,
                         tone_gain=1.0,
+                        sonar_db_transform=False,
+                        sonar_clahe=False,
+                        sonar_clahe_global=True,
+                        sonar_clahe_clip_limit=0.01,
                         wcp=False,
                         wcm=False,
                         wcr=False,
@@ -368,6 +372,12 @@ def rectify_master_func(logfilename='',
         son.rect_wcr = rect_wcr
         son.export_16bit = bool(export_16bit) and (not bool(getattr(son, 'son8bit', True)))
         son.export_colormap_uint8 = bool(export_colormap_uint8)
+        son.sonar_db_transform = bool(sonar_db_transform)
+        son.sonar_clahe = bool(sonar_clahe)
+        son.sonar_clahe_global = bool(sonar_clahe_global)
+        son.sonar_clahe_clip_limit = float(sonar_clahe_clip_limit)
+        if son.sonar_clahe:
+            son._ensure_clahe_global_bounds()
 
     # ############################################################################
     # # Rectify Heading sonar imagery - Pingwise, not Rubbersheeting             #
@@ -462,6 +472,12 @@ def rectify_master_func(logfilename='',
     for son in portstar:
         son.rect_wcp = rect_wcp
         son.rect_wcr = rect_wcr
+        son.sonar_db_transform = bool(sonar_db_transform)
+        son.sonar_clahe = bool(sonar_clahe)
+        son.sonar_clahe_global = bool(sonar_clahe_global)
+        son.sonar_clahe_clip_limit = float(sonar_clahe_clip_limit)
+        if son.sonar_clahe:
+            son._ensure_clahe_global_bounds()
 
     if (rect_wcp and rubberSheeting) or (rect_wcr and rubberSheeting):
         # Always use COG for rubber sheeting

pingmapper-5.5.3/pingmapper/version.py

@@ -0,0 +1 @@
+__version__ = '5.5.3'

{pingmapper-5.5.2 → pingmapper-5.5.3}/pingmapper.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.5.2
+Version: 5.5.3
 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-5.5.2/pingmapper/version.py

@@ -1 +0,0 @@
-__version__ = '5.5.2'