pingmapper 5.0.7__tar.gz → 5.0.9__tar.gz

{pingmapper-5.0.7 → pingmapper-5.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.0.7
+Version: 5.0.9
 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-5.0.7 → pingmapper-5.0.9}/pingmapper/class_portstarObj.py

@@ -59,9 +59,14 @@ import matplotlib.pyplot as plt
 
 import inspect
 
-from doodleverse_utils.imports import *
-from doodleverse_utils.model_imports import *
-from doodleverse_utils.prediction_imports import *
+try:
+    from doodleverse_utils.imports import *
+    from doodleverse_utils.model_imports import *
+    from doodleverse_utils.prediction_imports import *
+except ImportError:
+    print('Could not import Doodleverse Utils. Please install these packages to use PING-Mapper.')
+    print('They are not needed for GhostVision. Trying to continue...')
+    pass
 
 import geopandas as gpd
 

{pingmapper-5.0.7 → pingmapper-5.0.9}/pingmapper/class_sonObj.py

@@ -1301,7 +1301,10 @@ class sonObj(object):
 
                 # Distance (in meters)
                 d = sonMeta['trk_dist'].to_numpy()
-                d = np.max(d) - np.min(d)
+                # d = np.max(d) - np.min(d)
+                d = d[-1] - d[0]
+
+                
 
                 pixM = sonMeta['pixM']
                 # Find most common pixel size
@@ -1313,11 +1316,36 @@ class sonObj(object):
                 # Distance in pix
                 d = round(d / pixM, 0).astype(int)
 
-                sonDat = resize(sonDat,
-                                (sonDat.shape[0], d),
-                                mode='reflect',
-                                clip=True,
-                                preserve_range=True)
+                # to avoid oom errors
+                rows = sonDat.shape[0]
+                new_cols = d  # your target width
+                item_size = sonDat.itemsize  # bytes per element
+
+                estimated_bytes = rows * new_cols * item_size
+                estimated_MB = estimated_bytes / 1e6
+
+                available_bytes = psutil.virtual_memory().available
+                available_MB = available_bytes / 1e6
+
+
+                mem_margin = 0.9
+                safe_limit_MB = available_MB * (1 - mem_margin)
+
+                if d > 0 and estimated_MB < safe_limit_MB and new_cols<65500:
+                    sonDat = resize(
+                        sonDat,
+                        (rows, new_cols),
+                        mode='reflect',
+                        clip=True,
+                        preserve_range=True
+                    )
+                if estimated_MB > safe_limit_MB:
+                    print(f"Resize skipped for chunk {chunk}: estimated {estimated_MB:.2f} MB exceeds safe limit of {safe_limit_MB:.2f} MB.")
+                    # Optionally: fallback to chunked resize or downsampling
+                elif new_cols>65500:
+                    print(f"Resize skipped for chunk {chunk}: Maximum supported image dimension is 65500 pixels.")
+                else:
+                    print(f"Resize skipped for chunk {chunk}: Vessel did not move.")
 
             else:
                 sonDat = resize(sonDat,

{pingmapper-5.0.7 → pingmapper-5.0.9}/pingmapper/funcs_model.py

@@ -42,22 +42,42 @@ from pingmapper.funcs_common import *
 os.environ['TF_CPP_MIN_LOG_LEVEL']='3'
 import json
 import numpy as np
-import tensorflow as tf
-import tensorflow.keras.backend as K
-from tensorflow.python.client import device_lib
+# import tensorflow as tf
+# import tensorflow.keras.backend as K
+# from tensorflow.python.client import device_lib
 
 import itertools
 
-from transformers import TFSegformerForSemanticSegmentation
-from transformers import logging
-logging.set_verbosity_error()
+# from transformers import TFSegformerForSemanticSegmentation
+# from transformers import logging
+# logging.set_verbosity_error()
 
-# Fixes depth detection warning
-tf.get_logger().setLevel('ERROR')
+# # Fixes depth detection warning
+# tf.get_logger().setLevel('ERROR')
 
-from doodleverse_utils.imports import *
-from doodleverse_utils.model_imports import *
-from doodleverse_utils.prediction_imports import *
+# from doodleverse_utils.imports import *
+# from doodleverse_utils.model_imports import *
+# from doodleverse_utils.prediction_imports import *
+
+try:
+    import tensorflow as tf
+    import tensorflow.keras.backend as K
+    from tensorflow.python.client import device_lib
+
+    from transformers import TFSegformerForSemanticSegmentation
+    from transformers import logging
+    logging.set_verbosity_error()
+
+    # Fixes depth detection warning
+    tf.get_logger().setLevel('ERROR')
+
+    from doodleverse_utils.imports import *
+    from doodleverse_utils.model_imports import *
+    from doodleverse_utils.prediction_imports import *
+except ImportError:
+    print('Could not import Tensorflow and/or Transformers. Please install these packages to use PING-Mapper.')
+    print('They are not needed for GhostVision. Trying to continue...')
+    pass
 
 ################################################################################
 # model_imports.py from segmentation_gym                                       #
@@ -93,6 +113,7 @@ def initModel(weights, configfile, USE_GPU=False):
     --------------------
     self._detectDepth()
     '''
+
     SEED=42
     np.random.seed(SEED)
     AUTO = tf.data.experimental.AUTOTUNE # used in tf.data.Dataset API

{pingmapper-5.0.7 → pingmapper-5.0.9}/pingmapper/gui_main.py

@@ -10,16 +10,16 @@ SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
 PACKAGE_DIR = os.path.dirname(SCRIPT_DIR)
 sys.path.append(PACKAGE_DIR)
 
-# # For Debug
-# from funcs_common import *
-# from main_readFiles import read_master_func
-# from main_rectify import rectify_master_func
-# from main_mapSubstrate import map_master_func
+# For Debug
+from funcs_common import *
+from main_readFiles import read_master_func
+from main_rectify import rectify_master_func
+from main_mapSubstrate import map_master_func
 
-from pingmapper.funcs_common import *
-from pingmapper.main_readFiles import read_master_func
-from pingmapper.main_rectify import rectify_master_func
-from pingmapper.main_mapSubstrate import map_master_func
+# from pingmapper.funcs_common import *
+# from pingmapper.main_readFiles import read_master_func
+# from pingmapper.main_rectify import rectify_master_func
+# from pingmapper.main_mapSubstrate import map_master_func
 
 import json
 import pandas as pd
@@ -763,24 +763,26 @@ def gui(batch: bool):
                 print('\n===========================================')
                 print('===========================================')
                 print('***** READING *****')
-                read_master_func(**params)
+                ss_chan_avail  = read_master_func(**params)
                 # read_master_func(sonFiles, humFile, projDir, t, nchunk, exportUnknown, wcp, wcr, detectDepth, smthDep, adjDep, pltBedPick, threadCnt)
 
-                if rect_wcp or rect_wcr or banklines or coverage or pred_sub or map_sub or export_poly:
-                    print('\n===========================================')
-                    print('===========================================')
-                    print('***** RECTIFYING *****')
-                    rectify_master_func(**params)
-                    # rectify_master_func(sonFiles, humFile, projDir, nchunk, rect_wcp, rect_wcr, mosaic, threadCnt)
-
-                #==================================================
-                #==================================================
-                if pred_sub or map_sub or export_poly or pltSubClass:
-                    print('\n===========================================')
-                    print('===========================================')
-                    print('***** MAPPING SUBSTRATE *****')
-                    print("working on "+projDir)
-                    map_master_func(**params)
+                if ss_chan_avail:
+
+                    if rect_wcp or rect_wcr or banklines or coverage or pred_sub or map_sub or export_poly:
+                        print('\n===========================================')
+                        print('===========================================')
+                        print('***** RECTIFYING *****')
+                        rectify_master_func(**params)
+                        # rectify_master_func(sonFiles, humFile, projDir, nchunk, rect_wcp, rect_wcr, mosaic, threadCnt)
+
+                    #==================================================
+                    #==================================================
+                    if pred_sub or map_sub or export_poly or pltSubClass:
+                        print('\n===========================================')
+                        print('===========================================')
+                        print('***** MAPPING SUBSTRATE *****')
+                        print("working on "+projDir)
+                        map_master_func(**params)
 
                 gc.collect()
                 print("\n\nTotal Processing Time: ",datetime.timedelta(seconds = round(time.time() - start_time, ndigits=0)))

{pingmapper-5.0.7 → pingmapper-5.0.9}/pingmapper/main_readFiles.py

@@ -36,17 +36,23 @@ SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
 PACKAGE_DIR = os.path.dirname(SCRIPT_DIR)
 sys.path.append(PACKAGE_DIR)
 
-# # For debug
-# from funcs_common import *
-# from class_sonObj import sonObj
-# from class_portstarObj import portstarObj
+# For debug
+from funcs_common import *
+from class_sonObj import sonObj
+from class_portstarObj import portstarObj
 
-from pingmapper.funcs_common import *
-from pingmapper.class_sonObj import sonObj
-from pingmapper.class_portstarObj import portstarObj
+# from pingmapper.funcs_common import *
+# from pingmapper.class_sonObj import sonObj
+# from pingmapper.class_portstarObj import portstarObj
 
 import shutil
-from doodleverse_utils.imports import *
+
+try:
+    from doodleverse_utils.imports import *
+except ImportError:
+    print('Could not import Doodleverse Utils. Please install these packages to use PING-Mapper.')
+    print('They are not needed for GhostVision. Trying to continue...')
+    pass
 
 from scipy.signal import savgol_filter
 
@@ -413,8 +419,34 @@ def read_master_func(logfilename='',
         if son.beamName == 'ss_port' or son.beamName == 'ss_star':
             ss_chan_avail.append(son)
     if len(ss_chan_avail) == 0:
-        print('\n\nNo side-scan channels available. Aborting!')
-        sys.exit()
+        # print('\n\nNo side-scan channels available. Aborting!')
+        # sys.exit()
+
+        print('\n\nNo side-scan channels available!\nUpdating processing parameters as necessary...')
+        print('\nFiltering not avaialable...')
+        max_heading_deviation = 0
+        min_speed = 0
+        max_speed = 0
+        aoi = ''
+        time_table = ''
+
+        print('\nAuto depth picking not available...')
+        detectDep = 0
+        pltBedPick = False
+
+        print('\nShadow removal not available')
+        remShadow = 0
+        pred_sub = False
+
+        print('\nEGN not available...')
+        egn = False
+
+        print('\nWCO and WCM not available...')
+        wco = False
+        wcm = False
+
+
+
     elif len(ss_chan_avail) == 1:
         print('\n\nMaking copy of {} to ensure PINGMapper compatibility'.format(son.beamName))
         origBeam = son.beamName
@@ -1015,8 +1047,12 @@ def read_master_func(logfilename='',
         saveDepth = False
 
     if saveDepth:
-        # Save detected depth to csv
-        depDF = psObj._saveDepth(chunks, detectDep, smthDep, adjDep, instDepAvail)
+
+        if ss_chan_avail:
+            # Save detected depth to csv
+            depDF = psObj._saveDepth(chunks, detectDep, smthDep, adjDep, instDepAvail)
+        else:
+            depDF = []
 
         # Store depths in downlooking sonar files also
         for son in sonObjs:
@@ -1495,3 +1531,9 @@ def read_master_func(logfilename='',
         son._pickleSon()
     gc.collect()
     printUsage()
+
+    if len(ss_chan_avail) == 0:
+        return False
+    else:
+        return True
+

pingmapper-5.0.9/pingmapper/version.py

@@ -0,0 +1 @@
+__version__ = '5.0.9'

{pingmapper-5.0.7 → pingmapper-5.0.9}/pingmapper.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.0.7
+Version: 5.0.9
 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-5.0.7/pingmapper/version.py

@@ -1 +0,0 @@
-__version__ = '5.0.7'