pingmapper 5.0.14__py3-none-any.whl → 5.0.16__py3-none-any.whl

pingmapper/class_portstarObj.py

@@ -63,10 +63,29 @@ try:
     from doodleverse_utils.imports import *
     from doodleverse_utils.model_imports import *
     from doodleverse_utils.prediction_imports import *
-except ImportError:
+except ImportError as e:
+    import traceback
+    print('\n' + '='*80)
     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
+    print('\nDetailed error information:')
+    print('-'*80)
+    print(f'Error Type: {type(e).__name__}')
+    print(f'Error Message: {str(e)}')
+    print('-'*80)
+    traceback.print_exc()
+    print('='*80 + '\n')
+except Exception as e:
+    import traceback
+    print('\n' + '='*80)
+    print('Unexpected error while importing Doodleverse Utils.')
+    print('Detailed error information:')
+    print('-'*80)
+    print(f'Error Type: {type(e).__name__}')
+    print(f'Error Message: {str(e)}')
+    print('-'*80)
+    traceback.print_exc()
+    print('='*80 + '\n')
 
 import geopandas as gpd
 
@@ -874,6 +893,14 @@ 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:

pingmapper/class_sonObj.py

@@ -1453,104 +1453,6 @@ class sonObj(object):
 
         return
 
-    # ======================================================================
-    def _exportMovWin(self,
-                      i : int,
-                      stride : int,
-                      tileType: list,
-                      pingMax: int,
-                      depMax: int):
-        
-        '''
-        '''
-
-        # Set chunk index
-        a_idx = i-1
-        b_idx = i
-
-        # Iterate each tile type
-        for t in tileType:
-            if t == 'wco':
-                cropMax = depMax
-            else:
-                cropMax = pingMax
-            inDir = os.path.join(self.outDir, t)
-            outDir = os.path.join(self.outDir, t+'_mw')
-
-            if not os.path.exists(outDir):
-                try:
-                    os.mkdir(outDir)
-                except:
-                    pass
-
-            # Find the images
-            images = os.listdir(inDir)
-            images.sort()
-
-            # Get each image
-            a_img = images[a_idx]
-            b_img = images[b_idx]
-
-            # Get image name
-            img_name = a_img.split('.')[0]
-
-            # Open each image
-            a_img = imread(os.path.join(inDir, a_img))
-            b_img = imread(os.path.join(inDir, b_img))
-
-            def resize_to_pingMax(img, cropMax):
-                ndims = img.ndim
-                current_size = img.shape[0]
-                if current_size < cropMax:
-                    # Pad with zeros 
-                    if ndims == 2:
-                        padding = ((0, cropMax - current_size), (0, 0))
-                    else:
-                        padding = ((0, cropMax - current_size), (0, 0), (0,0))
-                    resized_img = np.pad(img, padding, mode='constant', constant_values=0)
-                elif current_size > cropMax:
-                    # Truncate the array
-                    resized_img = img[:cropMax, :]
-                else:
-                    # No change needed
-                    resized_img = img
-                return resized_img
-
-            # Resize a_img and b_img
-            a_img = resize_to_pingMax(a_img, cropMax)
-            b_img = resize_to_pingMax(b_img, cropMax)
-
-            # Set stride based on first image
-            # stride = int(round(a_img.shape[1] * stride, 0))
-            if stride == 0:
-                to_stride = 1
-            else:
-                to_stride = int(round(self.nchunk * stride, 0))
-
-            # Set window size based on first image
-            # winSize = a_img.shape[1]
-            winSize = self.nchunk
-
-            # Concatenate images
-            movWin = np.concatenate((a_img, b_img), axis=1)
-
-            # Last window idx
-            lastWinIDX = self.nchunk
-
-            win = 0
-            # Iterate each window
-            while win < lastWinIDX:
-                window = movWin[:, win:win+winSize]
-
-                zero = self._addZero(win)
-
-                # Save window
-                imsave(os.path.join(outDir, img_name+'_'+zero+str(win)+'.jpg'), window)
-
-                win += to_stride
-
-        return
-
 
     
     ############################################################################

pingmapper/funcs_model.py

@@ -59,6 +59,9 @@ import itertools
 # from doodleverse_utils.model_imports import *
 # from doodleverse_utils.prediction_imports import *
 
+# Flag to track if depth detection dependencies are available
+DEPTH_DETECTION_AVAILABLE = False
+
 try:
     import tensorflow as tf
     import tensorflow.keras.backend as K
@@ -74,10 +77,33 @@ try:
     from doodleverse_utils.imports import *
     from doodleverse_utils.model_imports import *
     from doodleverse_utils.prediction_imports import *
-except ImportError:
+    
+    DEPTH_DETECTION_AVAILABLE = True
+except ImportError as e:
+    import traceback
+    print('\n' + '='*80)
     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
+    print('\nDetailed error information:')
+    print('-'*80)
+    print(f'Error Type: {type(e).__name__}')
+    print(f'Error Message: {str(e)}')
+    print('-'*80)
+    traceback.print_exc()
+    print('='*80 + '\n')
+    DEPTH_DETECTION_AVAILABLE = False
+except Exception as e:
+    import traceback
+    print('\n' + '='*80)
+    print('Unexpected error while importing depth detection dependencies.')
+    print('Detailed error information:')
+    print('-'*80)
+    print(f'Error Type: {type(e).__name__}')
+    print(f'Error Message: {str(e)}')
+    print('-'*80)
+    traceback.print_exc()
+    print('='*80 + '\n')
+    DEPTH_DETECTION_AVAILABLE = False
 
 ################################################################################
 # model_imports.py from segmentation_gym                                       #
@@ -113,6 +139,13 @@ def initModel(weights, configfile, USE_GPU=False):
     --------------------
     self._detectDepth()
     '''
+    
+    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"
+        )
 
     SEED=42
     np.random.seed(SEED)

pingmapper/gui_main.py

@@ -10,12 +10,6 @@ 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
-
 from pingmapper.funcs_common import *
 from pingmapper.main_readFiles import read_master_func
 from pingmapper.main_rectify import rectify_master_func

pingmapper/main_mapSubstrate.py

@@ -35,12 +35,6 @@ 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_mapSubstrateObj import mapSubObj
-# from class_portstarObj import portstarObj
-# from funcs_model import *
-
 from pingmapper.funcs_common import *
 from pingmapper.class_mapSubstrateObj import mapSubObj
 from pingmapper.class_portstarObj import portstarObj
@@ -85,8 +79,6 @@ def map_master_func(logfilename='',
                     mask_wc=False,
                     spdCor=False,
                     maxCrop=False,
-                    moving_window=False,
-                    window_stride=0.1,
                     USE_GPU=False,
                     remShadow=0,
                     detectDep=0,

pingmapper/main_readFiles.py

@@ -36,12 +36,8 @@ 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
-
 from pingmapper.funcs_common import *
+from pingmapper.funcs_model import DEPTH_DETECTION_AVAILABLE
 from pingmapper.class_sonObj import sonObj
 from pingmapper.class_portstarObj import portstarObj
 
@@ -49,10 +45,29 @@ import shutil
 
 try:
     from doodleverse_utils.imports import *
-except ImportError:
+except ImportError as e:
+    import traceback
+    print('\n' + '='*80)
     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
+    print('\nDetailed error information:')
+    print('-'*80)
+    print(f'Error Type: {type(e).__name__}')
+    print(f'Error Message: {str(e)}')
+    print('-'*80)
+    traceback.print_exc()
+    print('='*80 + '\n')
+except Exception as e:
+    import traceback
+    print('\n' + '='*80)
+    print('Unexpected error while importing Doodleverse Utils.')
+    print('Detailed error information:')
+    print('-'*80)
+    print(f'Error Type: {type(e).__name__}')
+    print(f'Error Message: {str(e)}')
+    print('-'*80)
+    traceback.print_exc()
+    print('='*80 + '\n')
 
 from scipy.signal import savgol_filter
 
@@ -101,8 +116,6 @@ def read_master_func(logfilename='',
                      mask_wc=False,
                      spdCor=False,
                      maxCrop=False,
-                     moving_window=False,
-                     window_stride=0.1,
                      USE_GPU=False,
                      remShadow=0,
                      detectDep=0,
@@ -839,7 +852,7 @@ def read_master_func(logfilename='',
                 elif (att == "inst_dep_m") and (attAvg == 0): # Automatically detect depth if no instrument depth
                     valid=False
                     invalid[son.beam+"."+att] = False
-                    detectDep=0#1
+                    detectDep=1
                 else:
                     valid=False
                     invalid[son.beam+"."+att] = False
@@ -997,45 +1010,53 @@ def read_master_func(logfilename='',
     del son
 
     chunks = np.unique(chunks).astype(int)
-
     # # Automatically estimate depth
     if detectDep > 0:
-        print('\n\nAutomatically estimating depth for', len(chunks), 'chunks:')
+        # Check if depth detection dependencies are available
+        if 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.')
+            print('Please install them using: pip install tensorflow transformers doodleverse-utils')
+            print('Skipping automatic depth estimation...\n')
+            detectDep = 0
+        else:
+            print('\n\nAutomatically estimating depth for', len(chunks), 'chunks:')
 
-        #Dictionary to store chunk : np.array(depth estimate)
-        psObj.portDepDetect = {}
-        psObj.starDepDetect = {}
+            #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:
+            # 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))
+                # 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...')
+            # With binary thresholding
+            elif detectDep == 2:
+                print('\n\tUsing binary thresholding...')
 
-        # Parallel estimate depth for each chunk using appropriate method
-        r = Parallel(n_jobs=np.min([len(chunks), threadCnt]))(delayed(psObj._detectDepth)(detectDep, int(chunk), USE_GPU, tileFile) for chunk in tqdm(chunks))
+            # Parallel estimate depth for each chunk using appropriate method
+            r = Parallel(n_jobs=np.min([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
+            # 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
 
-        # Flag indicating depth autmatically estimated
-        autoBed = True
+            # Flag indicating depth autmatically estimated
+            autoBed = True
 
-        saveDepth = True
+            saveDepth = True
 
     # Don't estimate depth, use instrument depth estimate (sonar derived)
     elif detectDep == 0:
@@ -1067,9 +1088,10 @@ def read_master_func(logfilename='',
 
                 sonDF['dep_m_Method'] = 'Instrument Depth'
                 sonDF['dep_m_smth'] = False
-                sonDF['dep_m_adjBy'] = adjDep
-                
+                sonDF['dep_m_adjBy'] = adjDep  
+
                 dep = sonDF['inst_dep_m']
+
                 if smthDep:
                     dep = savgol_filter(dep, 51, 3)
 
@@ -1077,11 +1099,23 @@ def read_master_func(logfilename='',
                 dep[dep==0] = np.nan
                 dep = np.asarray(dep)
                 nans = np.isnan(dep)
-                dep[nans] = np.interp(np.flatnonzero(nans), np.flatnonzero(~nans), dep[~nans])
                 
-                sonDF['dep_m'] = dep + adjDep
+                # Only interpolate if there are valid (non-NaN) values
+                if np.any(~nans):
+                    # There are some valid values, so we can interpolate
+                    dep[nans] = np.interp(np.flatnonzero(nans), np.flatnonzero(~nans), dep[~nans])
+
+                    sonDF['dep_m'] = dep + adjDep
+
+                    sonDF.to_csv(son.sonMetaFile, index=False, float_format='%.14f')
+                else:
+                    # All values are NaN - cannot interpolate
+                    print("\nWarning: All instrument depth values are NaN or zero. Cannot interpolate depth.")
+                    print("This may indicate missing depth data in the sonar file.")
+                
+                # sonDF['dep_m'] = dep + adjDep
 
-                sonDF.to_csv(son.sonMetaFile, index=False, float_format='%.14f')
+                # sonDF.to_csv(son.sonMetaFile, index=False, float_format='%.14f')
                 del sonDF, son.sonMetaDF
                 son._cleanup()
 
@@ -1433,83 +1467,6 @@ def read_master_func(logfilename='',
                 #     son._exportTilesSpd(i, tileFile=imgType, spdCor=spdCor, mask_shdw=mask_shdw, maxCrop=maxCrop)
                 #     sys.exit()
 
-                if moving_window and not spdCor:
-
-                    # Crop all images to most common range
-                    son._loadSonMeta()
-                    sDF = son.sonMetaDF
-                    
-                    rangeCnt = np.unique(sDF['ping_cnt'], return_counts=True)
-                    pingMaxi = np.argmax(rangeCnt[1])
-                    pingMax = int(rangeCnt[0][pingMaxi])
-
-                    depCnt = np.unique(sDF['dep_m'], return_counts=True)
-                    depMaxi = np.argmax(depCnt[1])
-                    depMax = int(depCnt[0][depMaxi]/sDF['pixM'][0])
-                    depMax += 50
-
-
-                    # Remove first chunk
-                    chunks.sort()
-                    chunks = chunks[1:]
-
-                    # Get types of files exported
-                    tileType = []
-                    if son.wcp:
-                        tileType.append('wcp')
-                    if son.wcm:
-                        tileType.append('wcm')
-                    if son.wcr_src:
-                        tileType.append('src')
-                    if son.wco:
-                        tileType.append('wco')
-
-                    Parallel(n_jobs= np.min([len(chunks), threadCnt]))(delayed(son._exportMovWin)(i, stride=window_stride, tileType=tileType, pingMax=pingMax, depMax=depMax) for i in tqdm(chunks))
-
-                    # son._exportMovWin(chunks, 
-                    #                   stride=window_stride, 
-                    #                   tileType=tileType)
-
-                    for t in tileType:
-                        shutil.rmtree(os.path.join(son.outDir, t))
-
-                    # Create a movie
-                    if tileFile == '.mp4' and moving_window and not spdCor:
-                        for t in tileType:
-                            inDir = os.path.join(son.outDir, t+'_mw')
-
-                            imgs = os.listdir(inDir)
-                            imgs.sort()
-
-                            frame = cv2.imread(os.path.join(inDir, imgs[0]))
-                            height, width, layers = frame.shape
-
-                            outName = '_'.join(imgs[0].split('_')[:-2])
-                            vidPath = os.path.join(inDir, outName+tileFile)
-
-                            video = cv2.VideoWriter(vidPath, cv2.VideoWriter_fourcc(*'mp4v'), 3, (width, height))
-                            for image in imgs:
-                                frame = cv2.imread(os.path.join(inDir, image))
-
-                                # Pad end
-                                if frame.shape[1] < nchunk:
-                                    n_dims = frame.ndim
-                                    if n_dims == 2:
-                                        padding = ((0,0), (0, nchunk-frame.shape[1]))
-                                    else:
-                                        padding = ((0,0), (0, nchunk-frame.shape[1]), (0,0))
-                                    frame = np.pad(frame, padding, mode='constant', constant_values=0)
-
-                                video.write(frame)
-
-                            video.release()
-
-                            # Removs
-                            for image in imgs:
-                                os.remove(os.path.join(inDir, image))
-
-                            # shutil.rmtree(os.path.join(son.outDir, t))
-
                 son._pickleSon()
 
 

pingmapper/main_rectify.py

@@ -38,12 +38,6 @@ 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_rectObj import rectObj
-# from class_portstarObj import portstarObj
-# from funcs_rectify import smoothTrackline
-
 from pingmapper.funcs_common import *
 from pingmapper.class_rectObj import rectObj
 from pingmapper.class_portstarObj import portstarObj
@@ -90,8 +84,6 @@ def rectify_master_func(logfilename='',
                         mask_wc=False,
                         spdCor=False,
                         maxCrop=False,
-                        moving_window=False,
-                        window_stride=0.1,
                         USE_GPU=False,
                         remShadow=0,
                         detectDep=0,

pingmapper/version.py

@@ -1 +1 @@
-__version__ = '5.0.14'
+__version__ = '5.0.16'

{pingmapper-5.0.14.dist-info → pingmapper-5.0.16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.0.14
+Version: 5.0.16
 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-5.0.16.dist-info/RECORD

@@ -0,0 +1,23 @@
+pingmapper/__init__.py,sha256=8zLGg-DfQhnDl2Ky0n-zXpN-8e-g7iR0AcaI4l4Vvpk,32
+pingmapper/__main__.py,sha256=dgFUyR5ZtgcrSOkq0EdLj_OZVdBKzsP0iHw2V0791wM,1367
+pingmapper/class_mapSubstrateObj.py,sha256=txB9YqXfVgDFi628jo2F1RtEw1lCNR8wYpkhy94bn0U,37036
+pingmapper/class_portstarObj.py,sha256=LSdOypJT2USyM31NxBiY3EwWv-IxdoSr_SCCoEEVluc,108002
+pingmapper/class_rectObj.py,sha256=JSfSIa5hckvcB8uFMkBMa0Vz4J6aGPWq346RzowfiMQ,96327
+pingmapper/class_sonObj.py,sha256=YLAn2TPQeX1R8I4IxG2ri--bp3RMZHVM4F_Nhr3h3ww,78263
+pingmapper/class_sonObj_nadirgaptest.py,sha256=DSFgjEgpwPgDZslw0vXGGBNFYlcoUa2Ufbr8i_Uqdhc,76915
+pingmapper/funcs_common.py,sha256=0uZErbrWZ_jhOLOc-CT--8OX4eHF9qE_E5Wwy60aSvQ,15300
+pingmapper/funcs_model.py,sha256=K3dLDSqS7_4e0tzNy0jD9ms6Q7N14XrPFHMFUYmA6nI,9854
+pingmapper/funcs_rectify.py,sha256=bAFWbNr4dyOuQzF1j4Je-K4zxfJZUjISc0nYrOot8Ng,12418
+pingmapper/gui_main.py,sha256=yW50qv2pNM4C10_W2-uj881EAl9SX6h67GwxPSn-l9U,34682
+pingmapper/main_mapSubstrate.py,sha256=l16mSGiAyeOD2gUyFdTXcyRQhrOMJ_vy-wQzyAWHXzM,20967
+pingmapper/main_readFiles.py,sha256=WmuDzOL5XnPKtkFb7Y9wPfzY0RmdATBi9Q2DTwjxT8U,56117
+pingmapper/main_rectify.py,sha256=QEcnQBNRrp31Vl2EsInDW8J_rG-_fVNMcmkuL9o1waw,19953
+pingmapper/test_PINGMapper.py,sha256=-SYMsdK-tTodXp5dCFSWPn-KRN7-OjX6OwjQ2-8hQg0,14176
+pingmapper/test_time.py,sha256=uHT0mtLDP1J6w-snoELyk4UzZ2LrDeF6jGgJJVloalg,750
+pingmapper/version.py,sha256=fE94lNPi9fbu0LzNLyP7Ayj3pfFHkUrC276eqo_kiZI,22
+pingmapper-5.0.16.data/data/pingmapper_config/default_params.json,sha256=NCFcjj7MF0y7ur7ufX3qwmoPjav1ICEpsi8tzVJaqRw,1305
+pingmapper-5.0.16.dist-info/licenses/LICENSE,sha256=lowDp_th1CGR0Z224a-jYRi-oNFe_0fdldL3USXhX-k,1095
+pingmapper-5.0.16.dist-info/METADATA,sha256=2VVrSBaoaldHbG72cF02WKH0nAIJ4ddG3FEZpA3GdPc,9203
+pingmapper-5.0.16.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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pingmapper-5.0.14.dist-info/RECORD

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