pingmapper 5.4.3__tar.gz → 5.4.5__tar.gz

{pingmapper-5.4.3 → pingmapper-5.4.5}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.4.3
+Version: 5.4.5
 Summary: Open-source interface for processing recreation-grade side scan sonar datasets and reproducibly mapping benthic habitat
-Author: Daniel Buscombe
-Author-email: Cameron Bodine <bodine.cs@gmail.email>
+Author: Cameron Bodine, Daniel Buscombe, Iury T Simoes-Sousa
+Author-email: bodine.cs@gmail.email
 License-Expression: MIT
 Project-URL: Homepage, https://cameronbodine.github.io/PINGMapper/
 Project-URL: GitHub, https://github.com/CameronBodine/PINGMapper
@@ -32,6 +32,7 @@ Requires-Dist: doodleverse_utils>=0.0.39; extra == "ml"
 Requires-Dist: tensorflow<3,>=2.20; extra == "ml"
 Requires-Dist: tf-keras<3,>=2.20; extra == "ml"
 Requires-Dist: transformers<5,>=4.57; extra == "ml"
+Dynamic: author-email
 Dynamic: license-file
 Dynamic: requires-python
 

{pingmapper-5.4.3 → pingmapper-5.4.5}/pingmapper/class_rectObj.py

@@ -327,7 +327,10 @@ class rectObj(sonObj):
                     if self.egn_stretch > 0:
                         self._egnDoStretch()
 
-            img = self._reserve_zero_for_nodata(self.sonDat)
+            img = self._reserve_zero_for_nodata(
+                self.sonDat,
+                preserve_zeros=(not bool(getattr(self, 'son8bit', False))),
+            )
             img = self._prepare_export_uint16(img)
             vals = img[img > 0]
             if vals.size == 0:
@@ -1861,7 +1864,10 @@ class rectObj(sonObj):
             col = df[xPix].to_numpy().astype(int)
             data = df[sonCol].to_numpy()
             if son:
-                data = self._reserve_zero_for_nodata(data)
+                data = self._reserve_zero_for_nodata(
+                    data,
+                    preserve_zeros=(not bool(getattr(self, 'son8bit', False))),
+                )
             apply_post_rect_colormap = use_16bit and self._rect_colormap_selected(son=son)
             source_scale_bounds = None
             if apply_post_rect_colormap:
@@ -2721,7 +2727,10 @@ class rectObj(sonObj):
 
             img = self.sonDat.copy()
             if son:
-                img = self._reserve_zero_for_nodata(img)
+                img = self._reserve_zero_for_nodata(
+                    img,
+                    preserve_zeros=(not bool(getattr(self, 'son8bit', False))),
+                )
             apply_post_rect_colormap = use_16bit and self._rect_colormap_selected(son=son)
             source_scale_bounds = None
             if apply_post_rect_colormap:
@@ -2812,7 +2821,10 @@ class rectObj(sonObj):
 
             img = self.sonDat
             if son:
-                img = self._reserve_zero_for_nodata(img)
+                img = self._reserve_zero_for_nodata(
+                    img,
+                    preserve_zeros=(not bool(getattr(self, 'son8bit', False))),
+                )
             apply_post_rect_colormap = son and use_16bit and self._rect_colormap_selected(son=son)
             source_scale_bounds = None
             if apply_post_rect_colormap:

{pingmapper-5.4.3 → pingmapper-5.4.5}/pingmapper/class_sonObj.py

@@ -1819,14 +1819,6 @@ class sonObj(object):
 
     # ======================================================================
     def _prepare_export_uint16(self, data):
-        cached = getattr(self, 'sonDat16', None)
-        if cached is not None:
-            try:
-                if cached.shape == data.shape:
-                    return cached.astype(np.uint16, copy=False)
-            except Exception:
-                pass
-
         arr = np.asarray(data)
 
         if arr.dtype == np.uint16:
@@ -1931,12 +1923,15 @@ class sonObj(object):
         return bool(getattr(self, 'export_colormap_uint8', True))
 
     # ======================================================================
-    def _reserve_zero_for_nodata(self, data):
+    def _reserve_zero_for_nodata(self, data, preserve_zeros=False):
         arr = np.asarray(data)
 
         if arr.size == 0:
             return arr
 
+        if preserve_zeros:
+            return arr.copy()
+
         out = arr.copy()
 
         if np.issubdtype(out.dtype, np.floating):

{pingmapper-5.4.3 → pingmapper-5.4.5}/pingmapper/test_PINGMapper.py

@@ -90,10 +90,12 @@ def test(ds):
         print("1 = Short recording \n2 = Long recording \n\nSYNTAX: python test_PINGMapper.py <1 or 2>\n\n")
         sys.exit()
 
-    d = os.environ.get('PINGMAPPER_DATA_DIR',
-        os.environ.get('CONDA_PREFIX',
-            os.path.join(os.path.expanduser('~'), '.pingmapper')))
-    exampleDir = os.path.join(d, 'exampleData')
+    repo_root = PACKAGE_DIR
+    d = os.environ.get(
+        'PINGMAPPER_DATA_DIR',
+        os.path.join(repo_root, '.data'),
+    )
+    exampleDir = os.path.join(d, 'example_data')
     ds_path = os.path.join(exampleDir, ds_name)
     ds_path = os.path.normpath(ds_path)
 
@@ -120,7 +122,12 @@ def test(ds):
     # Path to data/output
     inFile = ds_path+'.DAT'
     sonPath = ds_path
-    projDir = os.path.join(user_home_path, 'Desktop', 'PINGMapper-'+ds_name)
+    proj_base_dir = os.environ.get(
+        'PINGMAPPER_TEST_OUTPUT_DIR',
+        os.path.join(d, 'test_runs'),
+    )
+
+    projDir = os.path.join(proj_base_dir, 'PINGMapper-'+ds_name)
 
     inFile = os.path.abspath(inFile)
     sonPath = os.path.abspath(sonPath)
@@ -239,7 +246,7 @@ def test(ds):
     if project_mode == 0:
         # Create new project
         if not os.path.exists(projDir):
-            os.mkdir(projDir)
+            os.makedirs(projDir, exist_ok=False)
         else:
             projectMode_1_inval()
 
@@ -248,7 +255,7 @@ def test(ds):
         if os.path.exists(projDir):
             shutil.rmtree(projDir)
 
-        os.mkdir(projDir)        
+        os.makedirs(projDir, exist_ok=False)
 
     elif project_mode == 2:
         # Update project

pingmapper-5.4.5/pingmapper/version.py

@@ -0,0 +1 @@
+__version__ = '5.4.5'

{pingmapper-5.4.3 → pingmapper-5.4.5}/pingmapper.egg-info/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.4.3
+Version: 5.4.5
 Summary: Open-source interface for processing recreation-grade side scan sonar datasets and reproducibly mapping benthic habitat
-Author: Daniel Buscombe
-Author-email: Cameron Bodine <bodine.cs@gmail.email>
+Author: Cameron Bodine, Daniel Buscombe, Iury T Simoes-Sousa
+Author-email: bodine.cs@gmail.email
 License-Expression: MIT
 Project-URL: Homepage, https://cameronbodine.github.io/PINGMapper/
 Project-URL: GitHub, https://github.com/CameronBodine/PINGMapper
@@ -32,6 +32,7 @@ Requires-Dist: doodleverse_utils>=0.0.39; extra == "ml"
 Requires-Dist: tensorflow<3,>=2.20; extra == "ml"
 Requires-Dist: tf-keras<3,>=2.20; extra == "ml"
 Requires-Dist: transformers<5,>=4.57; extra == "ml"
+Dynamic: author-email
 Dynamic: license-file
 Dynamic: requires-python
 

{pingmapper-5.4.3 → pingmapper-5.4.5}/pyproject.toml

@@ -10,8 +10,9 @@ readme = "README.md"
 license = "MIT"
 requires-python = ">=3.10"
 authors = [
-    { name = "Cameron Bodine", email = "bodine.cs@gmail.email" },
+    { name = "Cameron Bodine"},
     { name = "Daniel Buscombe" },
+    { name = "Iury T Simoes-Sousa"}
 ]
 classifiers = [
     "Development Status :: 5 - Production/Stable",

pingmapper-5.4.3/pingmapper/version.py

@@ -1 +0,0 @@
-__version__ = '5.4.3'