pingmapper 5.0.11__tar.gz → 5.0.13__tar.gz

{pingmapper-5.0.11 → pingmapper-5.0.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.0.11
+Version: 5.0.13
 Summary: Open-source interface for processing recreation-grade side scan sonar datasets and reproducibly mapping benthic habitat
 Author: Cameron Bodine, Daniel Buscombe
 Author-email: bodine.cs@gmail.email

{pingmapper-5.0.11 → pingmapper-5.0.13}/pingmapper/__main__.py

@@ -22,8 +22,6 @@ def main(process):
     # Process single sonar log
     if process == 'gui':
         print('\n\nLaunching gui for processing single sonar log...\n\n')
-        # from pingmapper.gui_main import gui
-        # gui()
         from pingmapper.gui_main import gui
         gui(batch=False)
 

{pingmapper-5.0.11 → pingmapper-5.0.13}/pingmapper/class_rectObj.py

@@ -1988,6 +1988,11 @@ class rectObj(sonObj):
             isChunk.iloc[chunk+1] = True
             trkMeta = trkMeta[isChunk].reset_index(drop=False)
 
+        # Set pixel resolution if 0
+        if pix_res == 0:
+            pix_res = trkMeta['pixM'].mode()[0]
+            do_resize = False
+
         # Filter sonMetaDF by chunk
         if not hasattr(self, 'sonMetaDF'):
             self._loadSonMeta()

{pingmapper-5.0.11 → pingmapper-5.0.13}/pingmapper/class_sonObj.py

@@ -797,6 +797,94 @@ class sonObj(object):
         self.sonDat = sonDat.astype(np.uint8)
         return
 
+    # def _loadSonChunk(self, df):
+    #     """
+    #     Read pings and apply per-ping gain normalization.
+    #     - Assumes gain index is in df['gain'] aligned with loop index i.
+    #     - Uses table_value = (gidx - 255) * 137 and unit_scale to convert to physical units.
+    #     - For 'dB' mode: undo applied gain by multiplying with 10^(-gain_dB/20).
+    #     - For 'linear' mode: subtract the (scaled) offset: dat_corrected = dat - phys_value.
+    #     """
+
+    #     # Configurable defaults (set on self if desired)
+    #     gain_mode = 'linear'         # 'dB' or 'linear'
+    #     unit_scale = 100.0  # divisor to convert table units -> dB or linear units
+
+    #     # Only apply for RSD files (your earlier check)
+    #     apply_gain = self.sonFile.lower().endswith(".rsd")
+    #     sonDat = np.zeros((int(self.pingMax), len(self.pingCnt)), dtype=np.int32)
+
+    #     with open(self.sonFile, "rb") as file:
+    #         for i in range(len(self.headIdx)):
+    #             if ~np.isnan(self.headIdx[i]):
+    #                 ping_len = min(int(self.pingCnt[i]), int(self.pingMax))
+    #                 if not self.son8bit:
+    #                     ping_len *= 2
+
+    #                 headIDX = int(self.headIdx[i])
+    #                 son_offset = int(self.son_offset[i])
+    #                 pingIdx = headIDX + son_offset
+
+    #                 file.seek(pingIdx)
+    #                 buffer = file.read(ping_len)
+
+    #                 if self.flip_port:
+    #                     buffer = buffer[::-1]
+
+    #                 # Read raw samples: big-endian in file per your original code
+    #                 if self.son8bit:
+    #                     dat = np.frombuffer(buffer, dtype=">u1").astype(np.float32)
+    #                 else:
+    #                     # read big-endian uint16, then convert to native-endian float32
+    #                     try:
+    #                         dat_be = np.frombuffer(buffer, dtype=">u2")
+    #                     except Exception:
+    #                         dat_be = np.frombuffer(buffer[:-1], dtype=">u2")
+    #                     # convert to native-endian 16-bit then to float
+    #                     dat = dat_be.astype(np.uint16).astype(np.float32)
+
+    #                 # Apply gain correction if appropriate
+    #                 if apply_gain and gain_mode in ("dB", "linear"):
+    #                     # read gain index from your df (ensure integer)
+    #                     try:
+    #                         gidx = int(df.iloc[i]["gain"])
+    #                     except Exception:
+    #                         gidx = 0
+    #                     gidx = max(0, min(255, gidx))
+
+    #                     # table value in raw units
+    #                     table_unit_value = (gidx - 255) * 137
+    #                     phys_value = table_unit_value / float(unit_scale)
+
+    #                     if gain_mode == "dB":
+    #                         # phys_value is gain in dB that was applied when recording.
+    #                         # To normalize, undo that gain: multiply by 10^(-gain_dB/20).
+    #                         scale = 10.0 ** (-phys_value / 20.0)
+    #                         dat_corr = dat * scale
+    #                     else:
+    #                         # Linear offset case: subtract the stored offset to undo it.
+    #                         dat_corr = dat - phys_value
+    #                 else:
+    #                     dat_corr = dat
+
+    #                 # Clip and store into integer array, keep dynamic range
+    #                 # Here we store into sonDat as int32 to avoid overflow during processing.
+    #                 n = len(dat_corr)
+    #                 sonDat[:n, i] = np.round(dat_corr).astype(np.int32)
+
+    #     # Finalize sonDat dtype choice: keep float-like behavior downstream by using float32,
+    #     # or map to uint8/uint16 if your pipeline expects those dtypes.
+    #     if self.son8bit:
+    #         # clip to 0..255 and save as uint8
+    #         self.sonDat = np.clip(sonDat, 0, 255).astype(np.uint8)
+    #     else:
+    #         # preserve range as uint16 (clip to uint16) if desired
+    #         self.sonDat = np.clip(sonDat, 0, 65535).astype(np.uint16)
+
+    #     return
+
+
+
     # ======================================================================
     def _WC_mask(self, i, son=True):
         '''

{pingmapper-5.0.11 → pingmapper-5.0.13}/pingmapper/default_params.json

@@ -2,6 +2,7 @@
     "inDir":"",
     "inFile":"",
     "projDir":"",
+    "projName":"",
     "project_mode":true,
     "tempC":10,
     "nchunk":500,

{pingmapper-5.0.11 → pingmapper-5.0.13}/pingmapper/gui_main.py

@@ -113,7 +113,7 @@ def gui(batch: bool):
 
     else:
         text_project = sg.Text('Project Name', size=(15,1))
-        in_project = sg.InputText(key='projName', size=(50,1), default_text=os.path.basename(default_params['projDir']))
+        in_project = sg.InputText(key='projName', size=(50,1), default_text=default_params['projName'])
 
         # Add to layout
         layout.append([text_project, in_project])

pingmapper-5.0.13/pingmapper/version.py

@@ -0,0 +1 @@
+__version__ = '5.0.13'

{pingmapper-5.0.11 → pingmapper-5.0.13}/pingmapper.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.0.11
+Version: 5.0.13
 Summary: Open-source interface for processing recreation-grade side scan sonar datasets and reproducibly mapping benthic habitat
 Author: Cameron Bodine, Daniel Buscombe
 Author-email: bodine.cs@gmail.email

pingmapper-5.0.11/pingmapper/version.py

@@ -1 +0,0 @@
-__version__ = '5.0.11'