improve documentation and deepskin interface

.gitignore

@@ -66,6 +66,7 @@ bin/
 build*/
 __pycache__/
 samples/
+checkpoints/
 
 # coverage
 .coverage

deepskin/__init__.py

@@ -2,6 +2,12 @@
 # -*- coding: utf-8 -*-
 
 from .__version__ import __version__
+# import the segmentation model
+from .model import deepskin_model
+# import the features for the wound monitoring
+from .features import evaluate_features
+# import the PWAT evaluator for the wound scoring
+from .pwat import evaluate_PWAT_score
 
 __author__  = ['Nico Curti']
 __email__ = ['nico.curti2@unibo.it']

deepskin/__main__.py

@@ -1,11 +1,18 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import sys
-import json
+import os
+import cv2
 import argparse
 
+# package version
 from .__version__ import __version__
+# segmentation model for wound identification
+from .model import wound_segmentation
+# constant values
+from .constants import GREEN_COLOR_CODE
+from .constants import RED_COLOR_CODE
+from .constants import RESET_COLOR_CODE
 
 __author__  = ['Nico Curti']
 __email__ = ['nico.curti2@unibo.it']
@@ -38,27 +45,112 @@ def parse_args ():
     help='Get the current version installed',
   )
 
+  # input image filename
+  parser.add_argument(
+    '--input', '-i',
+    dest='filepath',
+    required=False,
+    action='store',
+    default=None,
+    type=str,
+    help=(
+      'Input filename or path on which load the image. '
+      'Ref https://docs.opencv.org/4.x/d4/da8/group__imgcodecs.html for the list of '
+      'supported formats. '
+    )
+  )
+
+  # deepskin --verbose
+  parser.add_argument(
+    '--verbose', '-w',
+    dest='verbose',
+    required=False,
+    action='store_true',
+    default=True,
+    help='Enable/Disable the code logging',
+  )
+
   args = parser.parse_args()
 
   return args
 
-
 def main ():
 
   # get the cmd parameters
   args = parse_args()
 
+  if args.verbose:
+    print(fr'''{GREEN_COLOR_CODE}
+     _                     _    _
+    | |                   | |  (_)
+  __| | ___  ___ _ __  ___| | ___ _ __
+ / _` |/ _ \/ _ \ '_ \/ __| |/ / | '_ \
+| (_| |  __/  __/ |_) \__ \   <| | | | |
+ \__,_|\___|\___| .__/|___/_|\_\_|_| |_|
+                | |
+                |_|
+      {RESET_COLOR_CODE}''',
+      end='\n',
+      flush=True,
+    )
+
   # results if version is required
   if args.version:
     # print it to stdout
     print(f'Deepskin package v{__version__}',
-      end='\n', file=sys.stdout, flush=True
+      end='\n', flush=True
     )
     # exit success
     exit(0)
 
-  # exit success
-  exit(0)
+  if args.filepath is None:
+    print(
+      f'{RED_COLOR_CODE}deepskin Error: the following arguments are required: --input/-i, --weight/-w{RESET_COLOR_CODE}',
+      end='\n',
+      flush=True,
+    )
+    exit(1)
+  elif not os.path.exists(args.filepath):
+    print((
+      f'{RED_COLOR_CODE}deepskin Error:{RESET_COLOR_CODE} input image file not found\n'
+      f'Given: {args.filepath}'
+      ),
+      end='\n',
+      flush=True,
+    )
+    exit(1)
+
+  if args.verbose:
+    print(f'Load the input image...',
+      end='',
+      flush=True,
+    )
+
+  # load the image using opencv
+  bgr = cv2.imread(args.filepath)
+  # convert the image from BGR to RGB fmt
+  rgb = bgr[..., ::-1]
+
+  if args.verbose:
+    print(f' {GREEN_COLOR_CODE}[DONE]{RESET_COLOR_CODE}',
+      end='\n',
+      flush=True
+    )
+
+  # get the wound segmentation mask
+  wound_mask = wound_segmentation(
+    img=rgb,
+    tol=0.5,
+    verbose=args.verbose,
+  )
+
+  # compute the wound PWAT
+  pwat = evaluate_PWAT_score(
+    img=rgb,
+    wound_mask=wound_mask,
+    verbose=args.verbose,
+  )
+
 
 if __name__ == '__main__':
 

deepskin/constants.py

@@ -0,0 +1,202 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import platform
+
+__author__  = ['Nico Curti']
+__email__ = ['nico.curti2@unibo.it']
+
+__all__ = [
+  'CRLF',
+  'IMG_SIZE',
+  'GREEN_COLOR_CODE',
+  'ORANGE_COLOR_CODE',
+  'VIOLET_COLOR_CODE',
+  'RED_COLOR_CODE',
+  'RESET_COLOR_CODE',
+  'Deepskin_CENTER',
+  'Deepskin_SCALE',
+  'Deepskin_PWAT_PARAMS',
+  'Deepskin_PWAT_BIAS',
+]
+
+IMG_SIZE = 256
+GREEN_COLOR_CODE = '\033[38;5;40m'
+ORANGE_COLOR_CODE = '\033[38;5;208m'
+VIOLET_COLOR_CODE = '\033[38;5;141m'
+RED_COLOR_CODE = '\033[38;5;196m'
+RESET_COLOR_CODE = '\033[0m'
+CRLF = '\r\x1B[K' if platform.system() != 'Windows' else '\r'
+
+Deepskin_CENTER = {
+  'w_haralick0': 0.0002222729472489692,
+  'w_haralick1': 1890.1645598237635,
+  'w_haralick2': 0.39624571900533073,
+  'w_haralick3': 1699.7507631374451,
+  'w_haralick4': 0.05825257441765201,
+  'w_haralick5': 165.46789722033162,
+  'w_haralick6': 4859.627907301425,
+  'w_haralick7': 7.907375987459552,
+  'w_haralick8': 12.570986041853839,
+  'w_haralick9': 8.417852836481736e-05,
+  'w_haralick10': 5.955239259730355,
+  'w_haralick11': -0.2021242003064579,
+  'w_haralick12': 0.9619772153300806,
+  'p_haralick0': 0.0001498540696012536,
+  'p_haralick1': 1642.1494695401611,
+  'p_haralick2': 0.5552398117391217,
+  'p_haralick3': 1964.5852700529895,
+  'p_haralick4': 0.06078474835571498,
+  'p_haralick5': 205.18173777610355,
+  'p_haralick6': 6119.316957254933,
+  'p_haralick7': 8.187785208529927,
+  'p_haralick8': 13.10517714959607,
+  'p_haralick9': 8.513602245362374e-05,
+  'p_haralick10': 5.943323499089892,
+  'p_haralick11': -0.20929446749325206,
+  'p_haralick12': 0.9697884563910389,
+  'w_avgR': 0.5212469820939212,
+  'w_avgG': 0.27109229463921075,
+  'w_avgB': 0.21401858655694464,
+  'p_avgR': 0.5763267835303386,
+  'p_avgG': 0.3564247033287137,
+  'p_avgB': 0.3081093298977088,
+  'w_stdR': 0.09237739554699534,
+  'w_stdG': 0.10829318823674319,
+  'w_stdB': 0.09195912180260984,
+  'p_stdR': 0.10716071451169598,
+  'p_stdG': 0.1401474853536956,
+  'p_stdB': 0.13216593170513105,
+  'w_avgH': 0.06552020427372157,
+  'w_avgS': 0.5892058218823246,
+  'w_avgV': 0.5212469820939212,
+  'p_avgH': 0.09036986402266009,
+  'p_avgS': 0.48847457610644596,
+  'p_avgV': 0.5767915389925715,
+  'w_stdH': 0.11715889282107367,
+  'w_stdS': 0.11403082370522448,
+  'w_stdV': 0.09260579562238144,
+  'p_stdH': 0.1824778713170838,
+  'p_stdS': 0.1440560768776456,
+  'p_stdV': 0.10723952971997479,
+  'w_park': 0.28480298580007396,
+  'p_park': 0.22188344728430864,
+  'w_amparo': 0.03164616239230859,
+  'p_amparo': 0.03691944795994818,
+}
+
+Deepskin_SCALE = {
+  'w_haralick0': 0.0002325046095526415,
+  'w_haralick1': 1404.4257572010195,
+  'w_haralick2': 0.23078393134467157,
+  'w_haralick3': 965.2959521200373,
+  'w_haralick4': 0.023780274040611858,
+  'w_haralick5': 68.48109193307027,
+  'w_haralick6': 2630.755286941684,
+  'w_haralick7': 0.5066619026943684,
+  'w_haralick8': 1.4678491082231115,
+  'w_haralick9': 4.888152908641458e-05,
+  'w_haralick10': 0.5095925355951518,
+  'w_haralick11': 0.11575370812484267,
+  'w_haralick12': 0.06070190816734167,
+  'p_haralick0': 9.672668886112473e-05,
+  'p_haralick1': 953.4214077362369,
+  'p_haralick2': 0.21065800501136922,
+  'p_haralick3': 925.506077994615,
+  'p_haralick4': 0.018952140859000446,
+  'p_haralick5': 57.92742976496601,
+  'p_haralick6': 3173.260857014111,
+  'p_haralick7': 0.38873009569827843,
+  'p_haralick8': 0.8671021401509353,
+  'p_haralick9': 3.675366174882123e-05,
+  'p_haralick10': 0.39261737487581705,
+  'p_haralick11': 0.062112428576971634,
+  'p_haralick12': 0.03229774274624053,
+  'w_avgR': 0.16656629897564573,
+  'w_avgG': 0.14635937524567533,
+  'w_avgB': 0.11880385258454706,
+  'p_avgR': 0.13331435845295891,
+  'p_avgG': 0.11832798552663454,
+  'p_avgB': 0.13275959348198357,
+  'w_stdR': 0.03928345907627907,
+  'w_stdG': 0.045476869848503826,
+  'w_stdB': 0.046438403018434535,
+  'p_stdR': 0.04882281971219227,
+  'p_stdG': 0.049730916792113555,
+  'p_stdB': 0.05846673654613731,
+  'w_avgH': 0.0928823575050199,
+  'w_avgS': 0.16858715377732175,
+  'w_avgV': 0.1666455216195598,
+  'p_avgH': 0.1636084021024,
+  'p_avgS': 0.15054938267363227,
+  'p_avgV': 0.13390847886402646,
+  'w_stdH': 0.18810319877291057,
+  'w_stdS': 0.04483667865035873,
+  'w_stdV': 0.0391485600808012,
+  'p_stdH': 0.2047438529951371,
+  'p_stdS': 0.05252145976774261,
+  'p_stdV': 0.04903280080434655,
+  'w_park': 0.15173598777434077,
+  'p_park': 0.10460738864219321,
+  'w_amparo': 0.0455553377351849,
+  'p_amparo': 0.05808570032051939,
+}
+
+Deepskin_PWAT_PARAMS = {
+  'w_haralick0': -0.22608690262627693,
+  'w_haralick1': 0.8419020236399831,
+  'w_haralick2': 1.9840516080509525,
+  'w_haralick3': 0.0,
+  'w_haralick4': -0.014677772064076867,
+  'w_haralick5': 0.0,
+  'w_haralick6': -0.028192574114897707,
+  'w_haralick7': 0.033573325209037996,
+  'w_haralick8': 0.0,
+  'w_haralick9': 0.4454964606178141,
+  'w_haralick10': 0.6586148883190893,
+  'w_haralick11': -0.13888628129503355,
+  'w_haralick12': 0.0,
+  'p_haralick0': 0.0,
+  'p_haralick1': 0.17821612965307904,
+  'p_haralick2': 0.0,
+  'p_haralick3': 0.0,
+  'p_haralick4': 0.0,
+  'p_haralick5': 0.0,
+  'p_haralick6': -0.010119483685282258,
+  'p_haralick7': 0.327880140420109,
+  'p_haralick8': 0.0,
+  'p_haralick9': -0.25511946678446584,
+  'p_haralick10': 0.10776636887371593,
+  'p_haralick11': 0.0,
+  'p_haralick12': 0.0,
+  'w_avgR': -0.11711651785031672,
+  'w_avgG': 2.1350537406274075,
+  'w_avgB': -0.2800676295856026,
+  'p_avgR': -1.0264783767720724,
+  'p_avgG': 0.7963529644104094,
+  'p_avgB': 0.0,
+  'w_stdR': 0.0,
+  'w_stdG': -0.3488198067525097,
+  'w_stdB': -1.073605999704211,
+  'p_stdR': 0.0,
+  'p_stdG': 0.0,
+  'p_stdB': 0.0,
+  'w_avgH': -0.7512504032512959,
+  'w_avgS': 0.0,
+  'w_avgV': -2.044720823209275,
+  'p_avgH': 1.2681488355543602,
+  'p_avgS': 1.1481222816655834,
+  'p_avgV': 0.0,
+  'w_stdH': -0.5847556821893894,
+  'w_stdS': 0.02710634669502382,
+  'w_stdV': 0.3894296265346003,
+  'p_stdH': -0.05659291142960778,
+  'p_stdS': 0.07895362196139402,
+  'p_stdV': 0.11913258096905475,
+  'w_park': -1.5749437194228606,
+  'p_park': 0.0,
+  'w_amparo': 0.0712150447907629,
+  'p_amparo': 0.21322070485461567,
+}
+
+Deepskin_PWAT_BIAS = 14.244211150770264