pingmapper 5.3.4__tar.gz → 5.3.6__tar.gz

{pingmapper-5.3.4 → pingmapper-5.3.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.3.4
+Version: 5.3.6
 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>

{pingmapper-5.3.4 → pingmapper-5.3.6}/pingmapper/class_portstarObj.py

@@ -979,20 +979,20 @@ class portstarObj(object):
         self._depthZheng() or self._depthThreshold()
         '''
         
-        # Check if depth detection dependencies are available
-        if not DEPTH_DETECTION_AVAILABLE:
-            raise ImportError(
-                "TensorFlow, Transformers, and/or Doodleverse Utils are not installed. "
-                "These packages are required for automatic depth detection. "
-                "Please install them using: pip install tensorflow transformers doodleverse-utils"
-            )
-
-        # Open model configuration file
-        with open(self.configfile) as f:
-            config = json.load(f)
-        globals().update(config)
-
         if method == 1:
+            # Check if depth detection dependencies are available
+            if not DEPTH_DETECTION_AVAILABLE:
+                raise ImportError(
+                    "TensorFlow, Transformers, and/or Doodleverse Utils are not installed. "
+                    "These packages are required for ML depth detection. "
+                    "Use method=2 for binary-threshold depth picking instead."
+                )
+
+            # Open model configuration file
+            with open(self.configfile) as f:
+                config = json.load(f)
+            globals().update(config)
+
             if not hasattr(self, 'bedpickModel'):
                 # model = self._initModel(USE_GPU)
                 model = initModel(self.weights, self.configfile, USE_GPU)
@@ -1003,7 +1003,7 @@ class portstarObj(object):
         elif method == 2:
             self.port._loadSonMeta()
             self.star._loadSonMeta()
-            portDepPixCrop, starDepPixCrop, i = self._depthThreshold(i, tileFile)
+            portDepPixCrop, starDepPixCrop, i = self._depthThreshold(i)
 
         gc.collect()
         return portDepPixCrop, starDepPixCrop, i
@@ -1391,25 +1391,31 @@ class portstarObj(object):
         for son in portstar:
             # Load sonar intensity, standardize & rescale
             son._getScanChunkSingle(chunk)
-            img = son.sonDat
-            img = standardize(img, 0, 1, True)[:,:,-1].squeeze()
+            img = standardize(np.asarray(son.sonDat)).squeeze()
+            if img.ndim == 3:
+                img = img[:, :, -1]
             W, H = img.shape[1], img.shape[0]
 
             # Get chunks sonar metadata and instrument depth
-            isChunk = son.sonMetaDF['chunk_id']==1
+            isChunk = son.sonMetaDF['chunk_id'] == chunk
             sonMeta = son.sonMetaDF[isChunk].reset_index()
-            # acousticBed = round(sonMeta['inst_dep_m'] / sonMeta['pix_m'], 0).astype(int)
-            acousticBed = round(sonMeta['inst_dep_m'] / sonMeta['pixM'], 0).astype(int)
+            acoustic_depth = pd.to_numeric(sonMeta['inst_dep_m'], errors='coerce').to_numpy(dtype=float, copy=True)
+            acousticBed = np.round(acoustic_depth / sonMeta['pixM'].to_numpy(dtype=float, copy=True), 0)
+            acousticBed = acousticBed[np.isfinite(acousticBed) & (acousticBed > 0)]
 
             ##################################
             # Step 1 : Acoustic Bedpick Filter
             # Use acoustic bed pick to crop image
-            bedMin = max(min(acousticBed)-50, 0)
-            bedMax = max(acousticBed)+pix_buf
+            if acousticBed.size > 0:
+                bedMin = max(int(np.nanmin(acousticBed)) - 50, 0)
+                bedMax = int(np.nanmax(acousticBed)) + pix_buf
+            else:
+                bedMin = 0
+                bedMax = H
 
             cropMask = np.ones((H, W)).astype(int)
             cropMask[:bedMin,:] = 0
-            cropMask[bedMax:,:] = 0
+            cropMask[min(bedMax, H):,:] = 0
 
             # Mask the image with bed_mask
             imgMasked = img*cropMask
@@ -1464,7 +1470,7 @@ class portstarObj(object):
             imgBinaryMask[imgBinaryMask>0] = 1 # Now set all val's greater than 0 to 1 to create the mask
 
             # Now fill in above last row filled to make sure no gaps in bed pixels
-            lastRow = bedMax
+            lastRow = min(bedMax, H - 1)
             imgBinaryMask[lastRow] = True
             for i in range(W):
                 if imgBinaryMask[lastRow-1,i] == 0:
@@ -1509,10 +1515,10 @@ class portstarObj(object):
             bed[nans] = np.interp(x(nans), x(~nans), bed[~nans])
             bed = bed.astype(int)
 
-            if son.beamName == 'ss_port':
+            if str(son.beamName).startswith('ss_port'):
                 # self.portDepDetect[chunk] = bed
                 portDepPixCrop = bed
-            elif son.beamName == 'ss_star':
+            elif str(son.beamName).startswith('ss_star'):
                 # self.starDepDetect[chunk] = bed
                 starDepPixCrop = bed
 
@@ -1557,6 +1563,43 @@ class portstarObj(object):
                           Integer < 0 = decrease depth estimate by x pixels.
                           0 = use depth estimate with no adjustment.
         '''
+        def _format_depth_adjustment(pix_m_series):
+            pix_m = pd.to_numeric(pix_m_series, errors='coerce')
+            valid_pix = pix_m[np.isfinite(pix_m) & (pix_m > 0)]
+            if len(valid_pix) == 0:
+                return '0 pixels'
+            return str(float(adjDep) / float(valid_pix.iloc[0])) + ' pixels'
+
+        def _sync_trackline_depth(beam_obj, beam_df):
+            trk_file = os.path.join(beam_obj.metaDir, 'Trackline_Smth_' + beam_obj.beamName + '.csv')
+            if not os.path.exists(trk_file):
+                return
+
+            trk_df = pd.read_csv(trk_file)
+            if 'record_num' not in trk_df.columns or 'record_num' not in beam_df.columns:
+                return
+
+            depth_cols = ['record_num', 'dep_m']
+            if 'dep_m_Method' in beam_df.columns:
+                depth_cols.append('dep_m_Method')
+            if 'dep_m_smth' in beam_df.columns:
+                depth_cols.append('dep_m_smth')
+            if 'dep_m_adjBy' in beam_df.columns:
+                depth_cols.append('dep_m_adjBy')
+
+            depth_df = beam_df[depth_cols].drop_duplicates(subset=['record_num'], keep='last').set_index('record_num')
+            trk_df = trk_df.set_index('record_num')
+
+            trk_df['dep_m'] = depth_df['dep_m']
+            if 'dep_m_Method' in depth_df.columns:
+                trk_df['dep_m_Method'] = depth_df['dep_m_Method']
+            if 'dep_m_smth' in depth_df.columns:
+                trk_df['dep_m_smth'] = depth_df['dep_m_smth']
+            if 'dep_m_adjBy' in depth_df.columns:
+                trk_df['dep_m_adjBy'] = depth_df['dep_m_adjBy']
+
+            trk_df.reset_index().to_csv(trk_file, index=False, float_format='%.14f')
+
         # Load sonar metadata file
         self.port._loadSonMeta()
         portDF = self.port.sonMetaDF
@@ -1617,8 +1660,8 @@ class portstarObj(object):
             portDF['dep_m_smth'] = smthDep
             starDF['dep_m_smth'] = smthDep
 
-            portDF['dep_m_adjBy'] = str(adjDep / portDF['pixM']) + ' pixels'
-            starDF['dep_m_adjBy'] = str(adjDep / starDF['pixM']) + ' pixels'
+            portDF['dep_m_adjBy'] = _format_depth_adjustment(portDF['pixM'])
+            starDF['dep_m_adjBy'] = _format_depth_adjustment(starDF['pixM'])
 
         elif detectDep > 0:
             # Prepare depth detection dictionaries
@@ -1703,8 +1746,8 @@ class portstarObj(object):
             portDF['dep_m_smth'] = smthDep
             starDF['dep_m_smth'] = smthDep
 
-            portDF['dep_m_adjBy'] = str(adjDep / portDF['pixM']) + ' pixels'
-            starDF['dep_m_adjBy'] = str(adjDep / starDF['pixM']) + ' pixels'
+            portDF['dep_m_adjBy'] = _format_depth_adjustment(portDF['pixM'])
+            starDF['dep_m_adjBy'] = _format_depth_adjustment(starDF['pixM'])
 
         # Interpolate over nan's (and set zeros to nan)
         portDep = portDF['dep_m'].to_numpy(copy=True)
@@ -1730,6 +1773,8 @@ class portstarObj(object):
         # Export to csv
         portDF.to_csv(self.port.sonMetaFile, index=False, float_format='%.14f')
         starDF.to_csv(self.star.sonMetaFile, index=False, float_format='%.14f')
+        _sync_trackline_depth(self.port, portDF)
+        _sync_trackline_depth(self.star, starDF)
 
         try:
             # Take average of both estimates to store with downlooking sonar csv
@@ -2305,7 +2350,7 @@ class portstarObj(object):
                 dd = float(depth * depth)
                 row_arr = np.arange(depth, H_pred)
                 src_idx = np.round(
-                    np.sqrt(row_arr.astype(np.float64) ** 2 - dd)
+                    np.sqrt(row_arr.astype(np.float32) ** 2 - dd)
                 ).astype(int)
                 valid = src_idx < H_pred
                 rows_v = row_arr[valid]

{pingmapper-5.3.4 → pingmapper-5.3.6}/pingmapper/class_sonObj.py

@@ -1328,7 +1328,7 @@ class sonObj(object):
             row_arr = np.arange(depth, H)
             # Horizontal range index via Pythagorean theorem (vectorised)
             src_idx = np.round(
-                np.sqrt(row_arr.astype(np.float64) ** 2 - dd)
+                np.sqrt(row_arr.astype(np.float32) ** 2 - dd)
             ).astype(int)
 
             # Discard out-of-bounds indices
@@ -2919,7 +2919,7 @@ class sonObj(object):
         '''
 
         # Get sonDat
-        sonDat = self.sonDat.astype('float64')
+        sonDat = self.sonDat.astype('float32')
 
         # Create mask from zero values
         mask = np.where(sonDat == 0, 0, 1)

{pingmapper-5.3.4 → pingmapper-5.3.6}/pingmapper/class_sonObj_nadirgaptest.py

@@ -957,7 +957,7 @@ class sonObj(object):
             row_arr = np.arange(depth, H)
             # Horizontal range via Pythagorean theorem, plus nadir gap offset
             src_idx = np.round(
-                np.sqrt(row_arr.astype(np.float64) ** 2 - dd)
+                np.sqrt(row_arr.astype(np.float32) ** 2 - dd)
             ).astype(int) + nadirGap
 
             # Discard out-of-bounds indices
@@ -2356,7 +2356,7 @@ class sonObj(object):
         '''
 
         # Get sonDat
-        sonDat = self.sonDat.astype('float64')
+        sonDat = self.sonDat.astype('float32')
 
         # Create mask from zero values
         mask = np.where(sonDat == 0, 0, 1)

{pingmapper-5.3.4 → pingmapper-5.3.6}/pingmapper/doWork.py

@@ -293,6 +293,7 @@ def doWork(
             if ss_chan_avail:
                 rect_wcp = run_params.get('rect_wcp', False)
                 rect_wcr = run_params.get('rect_wcr', False)
+                force_rectify = run_params.get('force_rectify', False)
                 banklines = run_params.get('banklines', False)
                 coverage = run_params.get('coverage', False)
                 pred_sub = run_params.get('pred_sub', False)
@@ -301,11 +302,12 @@ def doWork(
                 plt_subclass = run_params.get('pltSubClass', False)
 
                 if not nav_available:
-                    if rect_wcp or rect_wcr or banklines or coverage or pred_sub or map_sub or export_poly or plt_subclass:
+                    if rect_wcp or rect_wcr or force_rectify or banklines or coverage or pred_sub or map_sub or export_poly or plt_subclass:
                         print('\nWARNING: Navigation info is unavailable for this recording.')
                         print('Skipping rectification and substrate mapping workflows (non-georeferenced sonogram-only processing).')
                     rect_wcp = False
                     rect_wcr = False
+                    force_rectify = False
                     banklines = False
                     coverage = False
                     pred_sub = False
@@ -313,7 +315,7 @@ def doWork(
                     export_poly = False
                     plt_subclass = False
 
-                if rect_wcp or rect_wcr or banklines or coverage or pred_sub or map_sub or export_poly:
+                if rect_wcp or rect_wcr or force_rectify or banklines or coverage or pred_sub or map_sub or export_poly:
                     print('\n===========================================')
                     print('===========================================')
                     print('***** RECTIFYING *****')

{pingmapper-5.3.4 → pingmapper-5.3.6}/pingmapper/funcs_common.py

@@ -31,6 +31,12 @@
 
 import os, sys, struct, gc, io, contextlib
 
+# Configure TensorFlow runtime defaults as early as possible so informational
+# startup messages do not leak to stderr before logging is initialized.
+os.environ.setdefault('TF_CPP_MIN_LOG_LEVEL', '3')
+os.environ.setdefault('TF_ENABLE_ONEDNN_OPTS', '0')
+os.environ.setdefault('AUTOGRAPH_VERBOSITY', '0')
+
 # Add 'pingmapper' to the path, may not need after pypi package...
 SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
 PACKAGE_DIR = os.path.dirname(SCRIPT_DIR)
@@ -97,13 +103,27 @@ import json
 
 import logging
 
-from tqdm import tqdm
+from tqdm import tqdm as _tqdm
 
 import subprocess
 
 # from funcs_pyhum_correct import doPyhumCorrections
 
 
+# =========================================================
+def tqdm(*args, **kwargs):
+    '''
+    Shared tqdm wrapper so CLI progress bars stay readable in the GUI console.
+    Use PINGMAPPER_TQDM_NCOLS to override the default width when needed.
+    '''
+    if 'ncols' not in kwargs:
+        try:
+            kwargs['ncols'] = int(os.environ.get('PINGMAPPER_TQDM_NCOLS', '80'))
+        except (TypeError, ValueError):
+            kwargs['ncols'] = 80
+    return _tqdm(*args, **kwargs)
+
+
 # =========================================================
 def safe_n_jobs(task_count, thread_count=0):
     '''
@@ -139,6 +159,7 @@ def quiet_tensorflow_warnings():
     Safe to call even if TensorFlow is not installed.
     '''
     os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
+    os.environ['TF_ENABLE_ONEDNN_OPTS'] = '0'
     os.environ['AUTOGRAPH_VERBOSITY'] = '0'
 
     logging.getLogger('tensorflow').setLevel(logging.ERROR)
@@ -443,7 +464,7 @@ def saveDefaultParams(values, user_params=None):
             return {k: _sanitize(val) for k, val in v.items()}
         if isinstance(v, (np.integer, np.int_, np.int64)):
             return int(v)
-        if isinstance(v, (np.floating, np.float64, np.float64)):
+        if isinstance(v, (np.floating, np.float32, np.float32)):
             return float(v)
         if isinstance(v, (np.ndarray, list, tuple)):
             return [_sanitize(x) for x in v]
@@ -516,7 +537,7 @@ class FastPiecewiseAffineTransform(PiecewiseAffineTransform):
             [self.affines[i].params for i in range(len(self._tesselation.simplices))]
         )
 
-        result = np.empty((n, 3), dtype=np.float64)
+        result = np.empty((n, 3), dtype=np.float32)
 
         # Process in batches to avoid large allocations in find_simplex and the
         # affine einsum, both of which scale with n_coords and can exceed several GiB.

{pingmapper-5.3.4 → pingmapper-5.3.6}/pingmapper/gui_main.py

@@ -2,11 +2,8 @@
 import sys, os
 import webbrowser
 
-PySimpleGUI_License = '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'
-try:
-    import FreeSimpleGUI as sg
-except ImportError:
-    import PySimpleGUI as sg
+
+import FreeSimpleGUI as sg
 import matplotlib.pyplot as plt
 
 # Add 'pingmapper' to the path, may not need after pypi package...

{pingmapper-5.3.4 → pingmapper-5.3.6}/pingmapper/main_mapSubstrate.py

@@ -110,7 +110,8 @@ def map_master_func(logfilename='',
                     banklines=False,
                     export_16bit=False,
                     export_16bit_colormap=False,
-                    export_colormap_uint8=True):
+                    export_colormap_uint8=True,
+                    **kwargs):
 
     '''
     Main script to map substrates from side scan sonar imagery.

{pingmapper-5.3.4 → pingmapper-5.3.6}/pingmapper/main_readFiles.py

@@ -94,6 +94,17 @@ def _is_sidescan_beam(beam_name):
     return beam_name.startswith('ss_port') or beam_name.startswith('ss_star')
 
 
+def _sidescan_group_key(beam_name):
+    beam_name = str(beam_name)
+    if beam_name.startswith('ss_port_'):
+        return beam_name[len('ss_port_'):]
+    if beam_name.startswith('ss_star_'):
+        return beam_name[len('ss_star_'):]
+    if beam_name in {'ss_port', 'ss_star'}:
+        return 'default'
+    return beam_name
+
+
 #===========================================
 def read_master_func(logfilename='',
                      project_mode=0,
@@ -158,7 +169,9 @@ def read_master_func(logfilename='',
                      mosaic=False,
                      map_mosaic=0,
                      banklines=False,
-                     return_context=False):
+                     side_scan_only=False,
+                     return_context=False,
+                     **kwargs):
 
     '''
     Main script to read data from Humminbird sonar recordings. Scripts have been
@@ -353,7 +366,7 @@ def read_master_func(logfilename='',
     # Prepare Cerulean file for PINGMapper
     elif file_type == '.svlog':
         sonar_obj = cerul2pingmapper(inFile, projDir, nchunk, tempC, exportUnknown)
-        detectDep = 1 # No depth in cerulean files, so set to Zheng et al. 2021
+        detectDep = 1 if DEPTH_DETECTION_AVAILABLE else 2
         instDepAvail = False
 
     # Prepare JSF file for PINGMapper
@@ -374,6 +387,7 @@ def read_master_func(logfilename='',
         sys.exit()
 
     nav_available = bool(getattr(sonar_obj, 'has_position', True))
+    side_scan_only = bool(side_scan_only)
 
     # Sonar-only fallback for sources without navigation fields (e.g., some Cerulean logs).
     # Disable filters that rely on geospatial motion/position so processing can continue.
@@ -546,6 +560,19 @@ def read_master_func(logfilename='',
     else:
         pass
 
+    if side_scan_only:
+        if len(ss_chan_avail) == 0:
+            print('\n\nSide-scan only mode enabled, but no side-scan channels were recognized. Skipping processing.')
+            if return_context:
+                return {
+                    'has_sidescan': False,
+                    'has_nav': nav_available,
+                }
+            return False
+
+        print('\n\nSide-scan only mode enabled. Skipping non-side-scan channels.')
+        sonObjs = [son for son in sonObjs if _is_sidescan_beam(getattr(son, 'beamName', ''))]
+
     print(sonObjs)
     ####
     # OLD    
@@ -948,10 +975,15 @@ def read_master_func(logfilename='',
                     valid=True
                 elif (attMax != 0) or ("unknown" in att) or (att =="beam"):
                     valid=True
-                elif (att == "inst_dep_m") and (attAvg == 0): # Automatically detect depth if no instrument depth
-                    valid=False
-                    invalid[son.beam+"."+att] = False
-                    detectDep=1
+                elif att == "inst_dep_m":
+                    depth_values = pd.to_numeric(df[att], errors='coerce').to_numpy(dtype=float, copy=False)
+                    has_valid_instrument_depth = np.isfinite(depth_values).any() and np.nanmax(depth_values) > 0
+                    if not has_valid_instrument_depth: # Automatically detect depth if instrument depth is missing/empty
+                        valid=False
+                        invalid[son.beam+"."+att] = False
+                        detectDep = 1 if DEPTH_DETECTION_AVAILABLE else 2
+                    else:
+                        valid=True
                 else:
                     valid=False
                     invalid[son.beam+"."+att] = False
@@ -1096,17 +1128,23 @@ def read_master_func(logfilename='',
 
     start_time = time.time()
 
-    # Determine which sonObj is port/star
-    portstar = []
+    # Determine which sonObj pairs should be depth processed together.
+    sidescan_groups = {}
     for son in sonObjs:
-        beam = son.beamName
-        if _is_sidescan_beam(beam):
-            portstar.append(son)
+        beam = str(son.beamName)
+        if not _is_sidescan_beam(beam):
+            continue
+
+        group_key = _sidescan_group_key(beam)
+        group = sidescan_groups.setdefault(group_key, {})
+        if beam.startswith('ss_port'):
+            group['port'] = son
+        elif beam.startswith('ss_star'):
+            group['star'] = son
 
-    psObj = None
-    chunks = np.array([], dtype=int)
+    ps_depth_jobs = []
 
-    if len(portstar) == 0:
+    if len(sidescan_groups) == 0:
         print(
             '\n\nNo recognized side-scan channels available for depth processing. '\
             'Continuing with down-looking beams only.'
@@ -1116,20 +1154,28 @@ def read_master_func(logfilename='',
         pltBedPick = False
         remShadow = 0
     else:
-        # Create portstarObj
-        psObj = portstarObj(portstar)
+        for group_key, group in sorted(sidescan_groups.items()):
+            if 'port' not in group or 'star' not in group:
+                print(
+                    '\nSkipping side-scan depth group {} because a matching port/star pair was not found.'.format(group_key)
+                )
+                continue
+
+            psObj = portstarObj([group['port'], group['star']])
 
-        chunks = []
-        for son in portstar:
-            # Get chunk id's, ignoring those with nodata
-            c = son._getChunkID()
+            chunks = []
+            for son in [group['port'], group['star']]:
+                c = son._getChunkID()
+                chunks.extend(c)
+                del c
 
-            chunks.extend(c)
-            del c
+            chunks = np.unique(chunks).astype(int)
+            if len(chunks) == 0:
+                continue
 
-        chunks = np.unique(chunks).astype(int)
+            ps_depth_jobs.append((group_key, psObj, chunks))
 
-        if len(chunks) == 0:
+        if len(ps_depth_jobs) == 0:
             print(
                 '\n\nNo valid side-scan chunks available for depth processing. '\
                 'Continuing with down-looking beams only.'
@@ -1142,7 +1188,12 @@ def read_master_func(logfilename='',
     # # Automatically estimate depth
     if detectDep > 0:
         # Check if depth detection dependencies are available
-        if not DEPTH_DETECTION_AVAILABLE:
+        if detectDep == 1 and not DEPTH_DETECTION_AVAILABLE:
+            print('\n\nML depth detection dependencies are unavailable.')
+            print('Falling back to binary-threshold depth detection...\n')
+            detectDep = 2
+
+        if detectDep == 1 and not DEPTH_DETECTION_AVAILABLE:
             print('\n\nCannot estimate depth automatically:')
             print('TensorFlow, Transformers, and/or Doodleverse Utils are not installed.')
             print('These packages are required for automatic depth detection.')
@@ -1152,37 +1203,28 @@ def read_master_func(logfilename='',
             autoBed = False
             saveDepth = True
         else:
-            print('\n\nAutomatically estimating depth for', len(chunks), 'chunks:')
-
-            #Dictionary to store chunk : np.array(depth estimate)
-            psObj.portDepDetect = {}
-            psObj.starDepDetect = {}
-
-            # Estimate depth using:
-            # Zheng et al. 2021
-            # Load model weights and configuration file
-            if detectDep == 1:
-
-                # Store configuration file and model weights
-                # These were downloaded at the beginning of the script
-                depthModelVer = 'Bedpick_Zheng2021_Segmentation_unet_v1.0'
-                psObj.configfile = os.path.join(modelDir, depthModelVer, 'config', depthModelVer+'.json')
-                psObj.weights = os.path.join(modelDir, depthModelVer, 'weights', depthModelVer+'_fullmodel.h5')
-                print('\n\tUsing Zheng et al. 2021 method. Loading model:', os.path.basename(psObj.weights))
-
-            # With binary thresholding
-            elif detectDep == 2:
-                print('\n\tUsing binary thresholding...')
-
-            # Parallel estimate depth for each chunk using appropriate method
-            r = Parallel(n_jobs=safe_n_jobs(len(chunks), threadCnt))(delayed(psObj._detectDepth)(detectDep, int(chunk), USE_GPU, tileFile) for chunk in tqdm(chunks))
-
-            # store the depth predictions in the class
-            for ret in r:
-                psObj.portDepDetect[ret[2]] = ret[0]
-                psObj.starDepDetect[ret[2]] = ret[1]
-                del ret
-            del r
+            total_chunks = sum(len(chunks) for _, _, chunks in ps_depth_jobs)
+            print('\n\nAutomatically estimating depth for', total_chunks, 'chunks across', len(ps_depth_jobs), 'side-scan group(s):')
+
+            for group_key, psObj, chunks in ps_depth_jobs:
+                psObj.portDepDetect = {}
+                psObj.starDepDetect = {}
+
+                if detectDep == 1:
+                    depthModelVer = 'Bedpick_Zheng2021_Segmentation_unet_v1.0'
+                    psObj.configfile = os.path.join(modelDir, depthModelVer, 'config', depthModelVer+'.json')
+                    psObj.weights = os.path.join(modelDir, depthModelVer, 'weights', depthModelVer+'_fullmodel.h5')
+                    print('\n\tGroup {}: Using Zheng et al. 2021 method. Loading model: {}'.format(group_key, os.path.basename(psObj.weights)))
+                elif detectDep == 2:
+                    print('\n\tGroup {}: Using binary thresholding...'.format(group_key))
+
+                r = Parallel(n_jobs=safe_n_jobs(len(chunks), threadCnt))(delayed(psObj._detectDepth)(detectDep, int(chunk), USE_GPU, tileFile) for chunk in tqdm(chunks))
+
+                for ret in r:
+                    psObj.portDepDetect[ret[2]] = ret[0]
+                    psObj.starDepDetect[ret[2]] = ret[1]
+                    del ret
+                del r
 
             # Flag indicating depth autmatically estimated
             autoBed = True
@@ -1200,9 +1242,10 @@ def read_master_func(logfilename='',
 
     if saveDepth:
 
-        if ss_chan_avail and psObj is not None:
-            # Save detected depth to csv
-            depDF = psObj._saveDepth(chunks, detectDep, smthDep, adjDep, instDepAvail)
+        if ss_chan_avail and len(ps_depth_jobs) > 0:
+            depDF = []
+            for _, psObj, chunks in ps_depth_jobs:
+                depDF.append(psObj._saveDepth(chunks, detectDep, smthDep, adjDep, instDepAvail))
         else:
             depDF = []
 
@@ -1259,7 +1302,7 @@ def read_master_func(logfilename='',
         del depDF
 
         # Cleanup
-        if psObj is not None:
+        for _, psObj, _ in ps_depth_jobs:
             psObj._cleanup()
 
         print("\nDone!")

pingmapper-5.3.6/pingmapper/version.py

@@ -0,0 +1 @@
+__version__ = '5.3.6'

{pingmapper-5.3.4 → pingmapper-5.3.6}/pingmapper.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.3.4
+Version: 5.3.6
 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>

pingmapper-5.3.4/pingmapper/version.py

@@ -1 +0,0 @@
-__version__ = '5.3.4'