pingmapper 5.2.1__tar.gz → 5.3.1__tar.gz

{pingmapper-5.2.1 → pingmapper-5.3.1}/PKG-INFO

@@ -1,39 +1,38 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.2.1
+Version: 5.3.1
 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
-Project-URL: Issues, https://github.com/CameronBodine/PINGMapper/issues
-Project-URL: GitHub, https://github.com/CameronBodine/PINGMapper
+Author: Daniel Buscombe
+Author-email: Cameron Bodine <bodine.cs@gmail.email>
+License-Expression: MIT
 Project-URL: Homepage, https://cameronbodine.github.io/PINGMapper/
+Project-URL: GitHub, https://github.com/CameronBodine/PINGMapper
+Project-URL: Issues, https://github.com/CameronBodine/PINGMapper/issues
 Keywords: pingmapper,sonar,ecology,remotesensing,sidescan,sidescan-sonar,aquatic,humminbird,lowrance,gis,oceanography,limnology
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Classifier: Topic :: Scientific/Engineering :: Oceanography
 Classifier: Topic :: Scientific/Engineering :: GIS
 Classifier: Topic :: Scientific/Engineering :: Hydrology
-Requires-Python: >=3.6
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: pinginstaller
-Requires-Dist: pingwizard
-Requires-Dist: pingverter
-Dynamic: author
-Dynamic: author-email
-Dynamic: classifier
-Dynamic: description
-Dynamic: description-content-type
-Dynamic: keywords
+Requires-Dist: pinginstaller<3,>=2
+Requires-Dist: pingwizard<2,>=1
+Requires-Dist: pingverter<3,>=2
+Requires-Dist: psutil<8,>=7
+Requires-Dist: opencv-python<5,>=4.12
+Requires-Dist: rsa<5,>=4.9
+Requires-Dist: FreeSimpleGUI<6,>=5
+Provides-Extra: ml
+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: license-file
-Dynamic: project-url
-Dynamic: requires-dist
-Dynamic: requires-python
-Dynamic: summary
 
 # PING-Mapper
 [![PyPI - Version](https://img.shields.io/pypi/v/pingmapper?style=flat-square&label=Latest%20Version%20(PyPi))](https://pypi.org/project/pingmapper/)
@@ -139,6 +138,34 @@ Continued support for PINGMapper and tools in the [PING Ecosystem](./docs/PINGEc
 
 **Advocates & Mentors**: Vincent Capone - [Black Laser Learning](https://blacklaserlearning.com/)
 
+## Quick Start
+
+### Option A: Conda
+
+Please see [Getting Started](https://cameronbodine.github.io/PINGMapper/docs/gettingstarted) for full instructions, or simply run:
+
+```bash
+conda env create -f pingmapper/conda/PINGMapper.yml
+conda activate ping
+python -m pingmapper gui
+```
+
+### Option B: Pixi
+
+[Pixi](https://pixi.sh) manages all dependencies (including GDAL) automatically from a single `pyproject.toml`.
+
+1. [Install pixi](https://pixi.sh)
+2. Clone and run:
+   ```bash
+   git clone https://github.com/CameronBodine/PINGMapper.git
+   cd PINGMapper
+   pixi run pingmapper  # Launches PINGWizard
+   ```
+3. For machine learning features (substrate mapping):
+   ```bash
+   pixi run -e full gui    # GUI with ML support
+   ```
+
 ## Ready to get started?
 
 Follow the installation and testing instructions to [Get Started!](https://cameronbodine.github.io/PINGMapper/docs/gettingstarted)

{pingmapper-5.2.1 → pingmapper-5.3.1}/README.md

@@ -102,6 +102,34 @@ Continued support for PINGMapper and tools in the [PING Ecosystem](./docs/PINGEc
 
 **Advocates & Mentors**: Vincent Capone - [Black Laser Learning](https://blacklaserlearning.com/)
 
+## Quick Start
+
+### Option A: Conda
+
+Please see [Getting Started](https://cameronbodine.github.io/PINGMapper/docs/gettingstarted) for full instructions, or simply run:
+
+```bash
+conda env create -f pingmapper/conda/PINGMapper.yml
+conda activate ping
+python -m pingmapper gui
+```
+
+### Option B: Pixi
+
+[Pixi](https://pixi.sh) manages all dependencies (including GDAL) automatically from a single `pyproject.toml`.
+
+1. [Install pixi](https://pixi.sh)
+2. Clone and run:
+   ```bash
+   git clone https://github.com/CameronBodine/PINGMapper.git
+   cd PINGMapper
+   pixi run pingmapper  # Launches PINGWizard
+   ```
+3. For machine learning features (substrate mapping):
+   ```bash
+   pixi run -e full gui    # GUI with ML support
+   ```
+
 ## Ready to get started?
 
 Follow the installation and testing instructions to [Get Started!](https://cameronbodine.github.io/PINGMapper/docs/gettingstarted)

{pingmapper-5.2.1 → pingmapper-5.3.1}/pingmapper/class_mapSubstrateObj.py

@@ -1059,7 +1059,7 @@ class mapSubObj(rectObj):
             c = int(c.split('_')[-1])
             toMap[c] = n
 
-        del npzDir, npzs, n, c
+        del npzDir, npzs
         return toMap
 
 

{pingmapper-5.2.1 → pingmapper-5.3.1}/pingmapper/funcs_common.py

@@ -52,7 +52,15 @@ from osgeo import gdal
 import pyproj
 
 if 'GDAL_DATA' not in os.environ:
-    os.environ['GDAL_DATA'] = os.path.join(f'{os.sep}'.join(sys.executable.split(os.sep)[:-1]), 'Library', 'share', 'gdal')
+    prefix = os.environ.get('CONDA_PREFIX', os.path.dirname(os.path.dirname(sys.executable)))
+    candidates = [
+        os.path.join(prefix, 'share', 'gdal'),            # conda/pixi on Linux/macOS
+        os.path.join(prefix, 'Library', 'share', 'gdal'),  # conda/pixi on Windows
+    ]
+    for _candidate in candidates:
+        if os.path.isdir(_candidate):
+            os.environ['GDAL_DATA'] = _candidate
+            break
 
 import rasterio
 import geopandas as gpd

{pingmapper-5.2.1 → pingmapper-5.3.1}/pingmapper/funcs_model.py

@@ -42,6 +42,14 @@ from pingmapper.funcs_common import *
 quiet_tensorflow_warnings()
 import json
 import numpy as np
+
+# Prevent the transformers/huggingface_hub libraries from making network calls
+# to huggingface.co to check for model updates. The model weights are stored
+# locally, so no internet access is needed. These flags can also be set as
+# system environment variables (TRANSFORMERS_OFFLINE=1, HF_HUB_OFFLINE=1)
+# before launching PINGMapper to achieve the same effect without a code change.
+os.environ.setdefault("TRANSFORMERS_OFFLINE", "1")
+os.environ.setdefault("HF_HUB_OFFLINE", "1")
 # import tensorflow as tf
 # import tensorflow.keras.backend as K
 # from tensorflow.python.client import device_lib
@@ -114,6 +122,47 @@ Utilities provided courtesy Dr. Dan Buscombe from segmentation_gym
 https://github.com/Doodleverse/segmentation_gym
 '''
 
+#=======================================================================
+def _build_segformer_from_config(id2label, num_classes, num_channels=3):
+    '''
+    Construct a SegFormer model (nvidia/mit-b0 backbone architecture) entirely
+    from a hardcoded local config, without contacting HuggingFace Hub.
+
+    The config values below are the canonical mit-b0 architecture spec.
+    The backbone weights loaded here are random initialisation — they are
+    immediately overwritten by model.load_weights() with the Zenodo-hosted
+    fine-tuned weights, so no HF-sourced weights are ever used.
+    '''
+    from transformers import TFSegformerForSemanticSegmentation, SegformerConfig
+
+    label2id = {label: id for id, label in id2label.items()}
+
+    config = SegformerConfig(
+        num_channels=num_channels,
+        num_encoder_blocks=4,
+        depths=[2, 2, 2, 2],
+        sr_ratios=[8, 4, 2, 1],
+        hidden_sizes=[32, 64, 160, 256],
+        patch_sizes=[7, 3, 3, 3],
+        strides=[4, 2, 2, 2],
+        num_attention_heads=[1, 2, 5, 8],
+        mlp_ratios=[4, 4, 4, 4],
+        hidden_act='gelu',
+        hidden_dropout_prob=0.0,
+        attention_probs_dropout_prob=0.0,
+        classifier_dropout_prob=0.1,
+        initializer_range=0.02,
+        drop_path_rate=0.1,
+        layer_norm_eps=1e-06,
+        decoder_hidden_size=256,
+        semantic_loss_ignore_index=255,
+        num_labels=num_classes,
+        id2label=id2label,
+        label2id=label2id,
+    )
+
+    return TFSegformerForSemanticSegmentation(config)
+
 #=======================================================================
 def initModel(weights, configfile, USE_GPU=False):
     '''
@@ -192,7 +241,16 @@ def initModel(weights, configfile, USE_GPU=False):
         id2label = {}
         for k in range(NCLASSES):
             id2label[k]=str(k)
-        model = segformer(id2label,num_classes=NCLASSES)
+        # SegFormer always uses 3 input channels: seg_file2tensor() converts
+        # single-channel images to 3-channel via np.dstack before inference,
+        # so the Zenodo weights are always saved with num_channels=3.
+        model = _build_segformer_from_config(id2label, NCLASSES, num_channels=3)
+        # Subclassed Keras models are lazy — variables don't exist until the
+        # first forward pass. Do a dummy call to build them so load_weights()
+        # can match the saved HDF5 file's variable names.
+        # Input to TFSegformer is NCHW: (batch, channels, height, width)
+        dummy = tf.zeros((1, 3, TARGET_SIZE[0], TARGET_SIZE[1]))
+        model(dummy, training=False)
 
     model.load_weights(weights)
     # model = compile_models([model[0]], MODEL)

{pingmapper-5.2.1 → pingmapper-5.3.1}/pingmapper/gui_main.py

@@ -3,11 +3,10 @@ import sys, os
 import webbrowser
 
 PySimpleGUI_License = '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'
-# try:
-#     import FreeSimpleGUI as sg
-# except ImportError:
-#     import PySimpleGUI as sg
-import PySimpleGUI as sg
+try:
+    import FreeSimpleGUI as sg
+except ImportError:
+    import PySimpleGUI as sg
 import matplotlib.pyplot as plt
 
 # Add 'pingmapper' to the path, may not need after pypi package...
@@ -51,8 +50,10 @@ def gui(batch: bool):
     primary_default_params = os.path.join(SCRIPT_DIR, "default_params.json")
 
     if not os.path.exists(primary_default_params):
-        d = os.environ['CONDA_PREFIX']
-        primary_default_params = os.path.join(d, 'pingmapper_config', 'default_params.json')
+        # Fallback: look in environment prefix (works with both conda and pixi)
+        prefix = os.environ.get('CONDA_PREFIX', '')
+        if prefix:
+            primary_default_params = os.path.join(prefix, 'pingmapper_config', 'default_params.json')
     
     default_params_file = os.path.join(SCRIPT_DIR, "user_params.json")
 

{pingmapper-5.2.1 → pingmapper-5.3.1}/pingmapper/main_mapSubstrate.py

@@ -243,6 +243,14 @@ def map_master_func(logfilename='',
     # For Substrate Prediction                                                 #
     ############################################################################
 
+    if pred_sub > 0 and not DEPTH_DETECTION_AVAILABLE:
+        print('\n\nCannot predict substrate automatically:')
+        print('TensorFlow, Transformers, and/or Doodleverse Utils are not installed.')
+        print('These packages are required for substrate prediction.')
+        print('Please install them using: pip install tensorflow transformers doodleverse-utils')
+        print('Skipping substrate prediction...\n')
+        pred_sub = 0
+
     if pred_sub > 0:
         start_time = time.time()
 
@@ -294,7 +302,11 @@ def map_master_func(logfilename='',
     # Fot Substrate Plotting                                                   #
     ############################################################################
 
-    print(pltSubClass)
+    if pltSubClass and not DEPTH_DETECTION_AVAILABLE:
+        print('\n\nCannot export substrate plots:')
+        print('TensorFlow, Transformers, and/or Doodleverse Utils are not installed.')
+        print('Skipping substrate plot export...\n')
+        pltSubClass = False
 
     if pltSubClass:
         start_time = time.time()

{pingmapper-5.2.1 → pingmapper-5.3.1}/pingmapper/main_readFiles.py

@@ -303,28 +303,7 @@ def read_master_func(logfilename='',
     modelDir = get_segmentation_model_dir()
     if not os.path.exists(modelDir):
         downloadSegmentationModelsv1_0(modelDir)
-        getSegformer = True
-    else:
-        getSegformer = False
-
-    ###############
-    # Get segformer
-    if getSegformer:
-        NCLASSES = 8
-        id2label = {}
-        for k in range(NCLASSES):
-            id2label[k] = str(k)
-        
-        # try downloading segformer pretrained model
-        try:
-            _ = segformer(id2label, NCLASSES)
-        except:
-            print('\n\n\n\n')
-            print('ERROR! Unable to download pretrained SegFormer model!')
-            print('Your network settings are blocking the download.')
-            print('Please try running on a different network.')
-            print('Once the script has been run successfully, you should be able')
-            print('to run PING-Mapper on the current network.')
+
 
 
     ###############################################
@@ -1136,6 +1115,8 @@ def read_master_func(logfilename='',
             print('Please install them using: pip install tensorflow transformers doodleverse-utils')
             print('Skipping automatic depth estimation...\n')
             detectDep = 0
+            autoBed = False
+            saveDepth = True
         else:
             print('\n\nAutomatically estimating depth for', len(chunks), 'chunks:')
 
@@ -1306,6 +1287,26 @@ def read_master_func(logfilename='',
         else:
             keepShadow = False
 
+    if remShadow > 0 and not DEPTH_DETECTION_AVAILABLE:
+        print('\n\nCannot detect shadows automatically:')
+        print('TensorFlow, Transformers, and/or Doodleverse Utils are not installed.')
+        print('These packages are required for automatic shadow detection.')
+        print('Please install them using: pip install tensorflow transformers doodleverse-utils')
+        print('Skipping automatic shadow detection...\n')
+        remShadow = 0
+        keepShadow = True
+        for son in sonObjs:
+            son.remShadow = 0
+
+    if pred_sub and not DEPTH_DETECTION_AVAILABLE:
+        print('\n\nCannot map substrate automatically:')
+        print('TensorFlow, Transformers, and/or Doodleverse Utils are not installed.')
+        print('These packages are required for substrate mapping.')
+        print('Please install them using: pip install tensorflow transformers doodleverse-utils')
+        print('Skipping substrate mapping...\n')
+        pred_sub = 0
+        map_sub = 0
+
     if remShadow > 0:
         start_time = time.time()
         print('\n\nAutomatically detecting shadows for', len(chunks), 'chunks:')

pingmapper-5.3.1/pingmapper/processing_scripts/main_batchDirectory_2024-01-18_0926.py

@@ -0,0 +1,314 @@
+# Part of PING-Mapper software
+#
+# Co-Developed by Cameron S. Bodine and Dr. Daniel Buscombe
+#
+# Inspired by PyHum: https://github.com/dbuscombe-usgs/PyHum
+#
+# MIT License
+#
+# Copyright (c) 2022-23 Cameron S. Bodine
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+import sys
+sys.path.insert(0, 'src')
+
+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
+
+import time
+import datetime
+
+# Get processing script's dir so we can save it to file
+scriptDir = os.getcwd()
+
+# For the logfile
+oldOutput = sys.stdout
+
+#============================================
+
+#######################
+# Start User Parameters
+#######################
+
+# Path to data/output
+inDir = r'./exampleData/' # Parent folder of sonar recordings
+outDir = r'./procData' # Parent folder for export files
+
+# *** IMPORTANT ****
+# Export Mode: project_mode
+## 0==NEW PROJECT: Create a new project. [DEFAULT]
+##      If project already exists, program will exit without any project changes.
+##
+## 1==OVERWRITE MODE: Create new project, regardless of previous project state.
+##      If project exists, it will be DELETED and reprocessed.
+##      If project does not exist, a new project will be created.
+project_mode = 1
+
+
+# General Parameters
+tempC = 10 #Temperature in Celsius
+nchunk = 500 #Number of pings per chunk
+cropRange = 0.0 #Crop imagery to specified range [in meters]; 0.0==No Cropping
+exportUnknown = False #Option to export Unknown ping metadata
+fixNoDat = True # Locate and flag missing pings; add NoData to exported imagery.
+threadCnt = 0 #Number of compute threads to use; 0==All threads; <0==(Total threads + threadCnt); >0==Threads to use up to total threads
+
+
+# Output Pixel Resolution [meters]
+pix_res_son = 0.05 # 0 = Default (~0.02 m)
+pix_res_map = 0.25 # 0 = Default (~0.02 m)
+
+
+# Position Corrections
+## Provide an x and y offset to account for position offset between
+## control head (or external GPS) and transducer.
+## Origin (0,0) is the location of control head (or external GPS)
+## X-axis runs from bow (fore, or front) to stern (aft, or rear) with positive offset towards the bow, negative towards stern
+## Y-axis runs from portside (left) to starboard (right), with negative values towards the portside, positive towards starboard
+## Z-offsets can be provided with `adjDep` below.
+x_offset = 0.0 # [meters]
+y_offset = 0.0 # [meters]
+
+
+# Sonar Intensity Corrections
+egn = True
+egn_stretch = 1 # 0==Min-Max; 1==% Clip
+egn_stretch_factor = 0.5 # If % Clip, the percent of histogram tails to clip (1.0 == 1%)
+
+
+# Sonogram Exports
+tileFile = '.jpg' # Img format for plots and sonogram exports
+wcp = True #Export tiles with water column present: 0==False; 1==True, side scan channels only; 2==True, all available channels.
+wcr = True #Export Tiles with water column removed (and slant range corrected): 0==False; 1==True, side scan channels only; 2==True, all available channels.
+
+
+# Speed corrected sonogram Exports
+lbl_set = 2 # Export images for labeling: 0==False; 1==True, keep water column & shadows; 2==True, remove water column & shadows
+spdCor = 1 # Speed correction: 0==No Speed Correction; 1==Stretch by GPS distance; !=1 or !=0 == Stretch factor.
+maxCrop = False # True==Ping-wise crop; False==Crop tile to max range.
+
+
+# Depth Detection and Shadow Removal Parameters
+remShadow = 2  # 0==Leave Shadows; 1==Remove all shadows; 2==Remove only bank shadows
+detectDep = 1 #0==Use Humminbird depth; 1==Auto detect depth w/ Zheng et al. 2021;
+## 2==Auto detect depth w/ Thresholding
+
+smthDep = True #Smooth depth before water column removal
+adjDep = 0 #Aditional depth adjustment (in pixels) for water column removaL
+pltBedPick = True #Plot bedpick on sonogram
+
+
+# Rectification Parameters
+rect_wcp = True #Export rectified tiles with water column present
+rect_wcr = True #Export rectified tiles with water column removed/slant range corrected
+son_colorMap = 'Greys_r' # Specify colorramp for rectified imagery. '_r'==reverse the ramp: https://matplotlib.org/stable/tutorials/colors/colormaps.html
+
+
+# Substrate Mapping
+pred_sub = 1 # Automatically predict substrates and save to npz: 0==False; 1==True, SegFormer Model
+pltSubClass = True # Export plots of substrate classification and predictions
+map_sub = 1 # Export substrate maps (as rasters): 0==False; 1==True. Requires substrate predictions saved to npz.
+export_poly = True # Convert substrate maps to shapefile: map_sub must be > 0 or raster maps previously exported
+map_predict = 0 #Export rectified tiles of the model predictions: 0==False; 1==Probabilities; 2==Logits. Requires substrate predictions saved to npz.
+map_class_method = 'max' # 'max' only current option. Take argmax of substrate predictions to get final classification.
+
+
+# Mosaic Exports
+mosaic_nchunk = 0 # Number of chunks per mosaic: 0=All chunks. Specifying a value >0 generates multiple mosaics if number of chunks exceeds mosaic_nchunk.
+mosaic = 1 #Export sonar mosaic; 0==Don't Mosaic; 1==Do Mosaic - GTiff; 2==Do Mosaic - VRT
+map_mosaic = 1 #Export substrate mosaic; 0==Don't Mosaic; 1==Do Mosaic - GTiff; 2==Do Mosaic - VRT
+
+
+# Miscellaneous Exports
+banklines = True # Export banklines from sonar imagery
+
+
+#####################
+# End User Parameters
+#####################
+
+#============================================
+# Normalize paths
+inDir = os.path.normpath(inDir)
+outDir = os.path.normpath(outDir)
+
+# Find all DAT and SON files in all subdirectories of inDir
+inFiles=[]
+for root, dirs, files in os.walk(inDir):
+    for file in files:
+        if file.endswith('.DAT'):
+            inFiles.append(os.path.join(root, file))
+
+inFiles = sorted(inFiles)
+
+for i, f in enumerate(inFiles):
+    print(i, ":", f)
+
+errorRecording = []
+for datFile in inFiles:
+    try:
+        copied_script_name = os.path.basename(__file__).split('.')[0]+'_'+time.strftime("%Y-%m-%d_%H%M")+'.py'
+        script = os.path.join(scriptDir, os.path.basename(__file__))
+
+        logfilename = 'log_'+time.strftime("%Y-%m-%d_%H%M")+'.txt'
+        
+        start_time = time.time()
+
+        inPath = os.path.dirname(datFile)
+        humFile = datFile
+        recName = os.path.basename(humFile).split('.')[0]
+        sonPath = humFile.split('.DAT')[0]
+        sonFiles = sorted(glob(sonPath+os.sep+'*.SON'))
+
+        projDir = os.path.join(outDir, recName)
+
+        params = {
+            'logfilename':logfilename,
+            'project_mode':project_mode,
+            'script':[script, copied_script_name],
+            'humFile':humFile,
+            'sonFiles':sonFiles,
+            'projDir':projDir,
+            'tempC':tempC,
+            'nchunk':nchunk,
+            'exportUnknown':exportUnknown,
+            'fixNoDat':fixNoDat,
+            'threadCnt':threadCnt,
+            'pix_res_son': pix_res_son,
+            'pix_res_map': pix_res_map,
+            'x_offset':x_offset,
+            'y_offset':y_offset,
+            'egn':egn,
+            'egn_stretch':egn_stretch,
+            'egn_stretch_factor':egn_stretch_factor,
+            'tileFile':tileFile,
+            'wcp':wcp,
+            'wcr':wcr,
+            'lbl_set':lbl_set,
+            'spdCor':spdCor,
+            'maxCrop':maxCrop,
+            'USE_GPU':False,
+            'remShadow':remShadow,
+            'detectDep':detectDep,
+            'smthDep':smthDep,
+            'adjDep':adjDep,
+            'pltBedPick':pltBedPick,
+            'rect_wcp':rect_wcp,
+            'rect_wcr':rect_wcr,
+            'son_colorMap':son_colorMap,
+            'pred_sub':pred_sub,
+            'map_sub':map_sub,
+            'export_poly':export_poly,
+            'map_predict':map_predict,
+            'pltSubClass':pltSubClass,
+            'map_class_method':map_class_method,
+            'mosaic_nchunk':mosaic_nchunk,
+            'mosaic':mosaic,
+            'map_mosaic':map_mosaic,
+            'banklines':banklines,
+            }
+        
+        globals().update(params)
+        
+        # =========================================================
+        # Determine project_mode
+        print(project_mode)
+        if project_mode == 0:
+            # Create new project
+            if not os.path.exists(projDir):
+                os.mkdir(projDir)
+            else:
+                projectMode_1_inval()
+
+        elif project_mode == 1:
+            # Overwrite existing project
+            if os.path.exists(projDir):
+                shutil.rmtree(projDir)
+
+            os.mkdir(projDir)        
+
+        elif project_mode == 2:
+            # Update project
+            # Make sure project exists, exit if not.
+            
+            if not os.path.exists(projDir):
+                projectMode_2_inval()
+
+        # =========================================================
+        # For logging the console output
+
+        logdir = os.path.join(projDir, 'logs')
+        if not os.path.exists(logdir):
+            os.makedirs(logdir)
+
+        logfilename = os.path.join(logdir, logfilename)
+
+        sys.stdout = Logger(logfilename)
+
+        print('\n\n', '***User Parameters***')
+        for k,v in params.items():
+            print("| {:<20s} : {:<10s} |".format(k, str(v)))
+
+        print('sonPath',sonPath)
+        print('\n\n\n+++++++++++++++++++++++++++++++++++++++++++')
+        print('+++++++++++++++++++++++++++++++++++++++++++')
+        print('***** Working On *****')
+        print(humFile)
+        print('Start Time: ', datetime.datetime.now().strftime('%Y-%m-%d %H:%M'))
+
+        print('\n===========================================')
+        print('===========================================')
+        print('***** READING *****')
+        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:
+            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)
+
+        sys.stdout.log.close()
+
+    except Exception as Argument:
+        unableToProcessError(logfilename)
+        print('\n\nCould not process:', datFile)
+
+    sys.stdout = oldOutput
+
+    gc.collect()
+    print("\n\nTotal Processing Time: ",datetime.timedelta(seconds = round(time.time() - start_time, ndigits=0)))
+
+if len(errorRecording) > 0:
+    print('\n\nUnable to process the following:')
+    for d in errorRecording:
+        print('\n',d)