Refactoring in progress on Supervisor and Jurse

.gitignore

@@ -1 +1,3 @@
-Enrichment
+Enrichment/
+__pycache__/
+Logs/

logger.py

@@ -0,0 +1,51 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# \file %filename%.py
+# \brief TODO
+# \author Florent Guiotte <florent.guiotte@gmail.com>
+# \version 0.1
+# \date 24 avril 2018
+#
+# from https://fangpenlin.com/posts/2012/08/26/good-logging-practice-in-python/
+
+import os
+import logging.config
+from pathlib import Path
+
+import yaml
+
+def setup_logging(
+    default_path='logging.yaml',
+    default_level=logging.WARN,
+    env_key='LOG_CFG'
+):
+    """Setup logging configuration
+
+    """
+    path = default_path
+    value = os.getenv(env_key, None)
+    if value:
+        path = value
+    if os.path.exists(path):
+        with open(path, 'rt') as f:
+            config = yaml.safe_load(f.read())
+        makedirs(config)
+        logging.config.dictConfig(config)
+    else:
+        logging.basicConfig(level=default_level)
+
+
+def makedirs(dic):
+    files = finddirs(dic)
+    for f in files:
+        d = Path(*f.parts[:-1])
+        d.mkdir(parents=True, exist_ok=True)
+
+def finddirs(dic, key='filename'):
+    r = list()
+    value = dic.get(key)
+    if value : r.append(Path(value))
+    for k, v in dic.items():
+        if isinstance(v, dict):
+            r.extend(finddirs(v))
+    return r

logging.yaml

@@ -0,0 +1,40 @@
+version: 1
+disable_existing_loggers: False
+formatters:
+    simple:
+        format: "%(asctime)s %(levelname)s %(name)s: %(message)s"
+
+handlers:
+    console:
+        class: logging.StreamHandler
+        level: INFO
+        formatter: simple
+        stream: ext://sys.stdout
+
+    info_file_handler:
+        class: logging.handlers.RotatingFileHandler
+        level: INFO
+        formatter: simple
+        filename: Logs/info.log
+        maxBytes: 10485760 # 10MB
+        backupCount: 20
+        encoding: utf8
+
+    error_file_handler:
+        class: logging.handlers.RotatingFileHandler
+        level: ERROR
+        formatter: simple
+        filename: Logs/errors.log
+        maxBytes: 10485760 # 10MB
+        backupCount: 20
+        encoding: utf8
+
+loggers:
+    my_module:
+        level: DEBUG
+        handlers: [console]
+        propagate: no
+
+root:
+    level: DEBUG
+    handlers: [console, info_file_handler, error_file_handler]

mockup.yml

@@ -7,7 +7,7 @@ detail: |
     générique. Il faut ajouter le chargement dynamique du protocole puis
     réusiner le fonctionnement du supervisor pour respecter l'esprit universel
     de minigrida.
-protocol: JurseSF
+protocol: Jurse
 expe:
   ground_truth: 
     raster: ./Data/ground_truth/2018_IEEE_GRSS_DFC_GT_TR.tif

protocols/__init__.py

@@ -0,0 +1,9 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# \file __init__.py
+# \brief TODO
+# \author Florent Guiotte <florent.guiotte@gmail.com>
+# \version 0.1
+# \date 09 sept. 2018
+#
+# TODO details

protocols/jurse.py

@@ -0,0 +1,122 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# \file jurse.py
+# \brief TODO
+# \author Florent Guiotte <florent.guiotte@gmail.com>
+# \version 0.1
+# \date 07 sept. 2018
+#
+# TODO details
+
+import hashlib
+import importlib
+from collections import OrderedDict
+import numpy as np
+import pandas as pd
+from sklearn import metrics
+# TODO: create package, use dev
+import sys
+sys.path.append('../triskele/python')
+import triskele
+from .protocol import Protocol, TestError
+
+
+class Jurse(Protocol):
+    """First JURSE test protocol for LiDAR classification with 2D maps.
+
+    This first protocol compute attribute profiles on the whole scene then
+    split in train and test for a random forest classifier.
+
+    """
+
+    def __init__(self, expe):
+        super().__init__(expe, self.__class__.__name__)
+
+    def _get_hashes(self):
+        hashes = OrderedDict()
+        glob = hashlib.sha1()
+
+        for k in ['ground_truth', 'descriptors_script',
+                  'cross_validation', 'classifier']:
+            val = str(self._expe[k]).encode('utf-8')
+            hashes[k] = hashlib.sha1(val).hexdigest()
+            glob.update(val)
+        hashes['global'] = glob.hexdigest()
+
+        return hashes
+
+    def _run(self):
+        self._log.info('Compute descriptors')
+        try:
+            descriptors = self._compute_descriptors()
+        except Exception:
+            raise TestError('Error occured during description')
+
+        self._log.info('Classify data')
+        try:
+            classification = self._compute_classificatin(descriptors)
+        except Exception:
+            raise TestError('Error occured during classification')
+
+        self._log.info('Run metrics')
+        self._metrics = self._run_metrics(classification, descriptors)
+
+    def _compute_descriptors(self):
+        script = self._expe['descriptors_script']
+
+        desc = importlib.import_module(script['name'])
+        att = desc.run(**script['parameters'])
+
+        return att
+
+    def _compute_classification(self, descriptors):
+        # Ground truth
+        gt = self._get_ground_truth()
+
+        # CrossVal and ML
+        cv = self._expe['cross_validation']
+        cl = self._expe['classifier']
+
+        cross_val = getattr(importlib.import_module(cv['package']), cv['name'])
+        classifier = getattr(importlib.import_module(cl['package']), cl['name'])
+
+        prediction = np.zeros_like(gt)
+
+        for xt, xv, yt, yv, ti in cross_val(gt, descriptors, **cv['parameters']):
+            rfc = classifier(**cl['parameters'])
+            rfc.fit(xt, yt)
+
+            ypred = rfc.predict(xv)
+
+            prediction[ti] = ypred
+
+        return prediction
+
+    def _get_ground_truth(self):
+        gt_expe = self._expe['ground_truth']
+        gt = triskele.read(gt_expe['raster'])
+
+        # Meta labeling
+        idx_map = np.arange(gt.max() + 1)
+
+        if 'meta_labels' in self._expe:
+            meta_idx = pd.read_csv(gt_expe['meta_labels'])
+            idx = np.array(meta_idx['index'])
+            midx = np.array(meta_idx['metaclass_index'])
+            idx_map[idx] = midx
+
+        return idx_map[gt]
+
+    def _run_metrics(self, classification, descriptors):
+        gt = self._get_ground_truth()
+
+        f = np.nonzero(classification)
+        pred = classification[f].ravel()
+        gt = gt[f].ravel()
+
+        results = OrderedDict()
+        results['dimension'] = descriptors.shape[-1]
+        results['overall_accuracy'] = float(metrics.accuracy_score(gt, pred))
+        results['cohen_kappa'] = float(metrics.cohen_kappa_score(gt, pred))
+
+        return results

protocols/jurse_default.py

@@ -1,30 +0,0 @@
-#!/usr/bin/python
-# -*- coding: utf-8 -*-
-# \file jurse_default.py
-# \brief TODO
-# \author Florent Guiotte <florent.guiotte@gmail.com>
-# \version 0.1
-# \date 07 sept. 2018
-#
-# TODO details
-
-import hashlib
-from protocol import Protocol
-
-class Jurse(Protocol):
-    def __init__(self, expe):
-        super().__init__(expe, self.__class__.__name__)
-
-    def _get_hashes(self):
-        hashes = OrderedDict()
-        hashes['global'] = 'Protocol did not override _get_hashes()'
-
-        glob = hashlib.sha1()
-
-        for k in ['ground_truth', 'descriptors_script', 'cross_validation', 'classifier']:
-            v = str(expe[k]).encode('utf-8')
-            hashes[k] = hashlib.sha1(v).hexdigest()
-            glob.update(v)
-        hashes['global'] = glob.hexdigest()
-
-        return hashes

protocols/protocol.py

@@ -12,21 +12,23 @@ import logging
 import time
 from collections import OrderedDict
 
+
 class Protocol:
     def __init__(self, expe, name=None):
         self._log = logging.getLogger(name)
         self._expe = expe
         self._name = name
         self._times = OrderedDict()
-        self._pt = time.process_time()
+        self._log.debug('expe loaded: {}'.format(self._expe))
 
     def get_hashes(self):
         self._log.info('Computing hashes')
         return(self._get_hashes())
 
     def run(self):
-        self._kronos = Kronos()
+        self._pt = time.process_time()
         self._run()
+# TODO: Strop process timer
 
     def get_results(self):
         self._get_results()
@@ -60,4 +62,3 @@ class Protocol:
 
 class TestError(Exception):
     pass
-

supervisor.py

@@ -20,25 +20,7 @@ from operator import itemgetter
 import traceback
 import logging
 import logger
-
+from protocols.protocol import TestError
-log = logging.getLogger('Supervisor [{}]'.format(os.uname()[1]))
-
-### Keep yaml ordered, newline string
-def setup_yaml():
-    """ https://stackoverflow.com/a/8661021 """
-    represent_dict_order = lambda self, data:  self.represent_mapping('tag:yaml.org,2002:map', data.items())
-    yaml.add_representer(OrderedDict, represent_dict_order)    
-  
-    """ https://stackoverflow.com/a/24291536 """
-    yaml.Dumper.org_represent_str = yaml.Dumper.represent_str
-    yaml.add_representer(str, repr_str, Dumper=yaml.Dumper)
-
-def repr_str(dumper, data):
-    if '\n' in data:
-        return dumper.represent_scalar(u'tag:yaml.org,2002:str', data, style='|')
-    return dumper.org_represent_str(data)
-
-
 
 ENRICHMENT_DIR = Path('./Enrichment/')
 TEST_DIR    = ENRICHMENT_DIR / 'Tests'
@@ -46,30 +28,61 @@ STAGING_DIR = ENRICHMENT_DIR / 'Staging'
 RESULT_DIR  = ENRICHMENT_DIR / 'Results'
 FAILED_DIR  = ENRICHMENT_DIR / 'Failed'
 
+log = logging.getLogger('Supervisor [{}]'.format(os.uname()[1]))
+
+def setup_yaml():
+    """ Keep yaml ordered, newline string
+    from https://stackoverflow.com/a/8661021
+    """
+    represent_dict_order = lambda self, data: self.represent_mapping('tag:yaml.org,2002:map', data.items())
+    yaml.add_representer(OrderedDict, represent_dict_order)
+
+    """ https://stackoverflow.com/a/24291536 """
+    yaml.Dumper.org_represent_str = yaml.Dumper.represent_str
+    yaml.add_representer(str, repr_str, Dumper=yaml.Dumper)
+
+
+def repr_str(dumper, data):
+    if '\n' in data:
+        return dumper.represent_scalar(u'tag:yaml.org,2002:str',
+                                       data, style='|')
+    return dumper.org_represent_str(data)
+
+
 def update_queue():
     tmp_queue = list()
     for child in TEST_DIR.iterdir():
         if child.is_file() and child.suffix == '.yml':
-            tmp_queue.append({'expe_file': child, 'priority': get_priority(child)})
+            tmp_queue.append({'expe_file': child,
+                              'priority': get_priority(child)})
 
     queue = sorted(tmp_queue, key=itemgetter('priority'))
     return queue
 
+
 def get_priority(yml_file):
     with open(yml_file) as f:
         expe = OrderedDict(yaml.safe_load(f))
     return expe['priority']
 
+
 def run(expe_file):
     log.info('Run test {}'.format(expe_file))
     with open(expe_file) as f:
         test = OrderedDict(yaml.safe_load(f))
 
+
+
     ### Stage test
 
     ### Load protocol
+    protocol = getattr(importlib.import_module('protocols.jurse'), test['protocol'])
+    experience = protocol(test['expe'])
+    log.info('{} test protocol loaded'.format(experience))
 
     ### Write hahes
+    hashes = experience.get_hashes()
+    log.info(hashes)
 
     ### Run test
 
@@ -80,12 +93,6 @@ def run(expe_file):
     ### End of test
     return
     
-    ### Keep track of time 
-    kronos = Kronos()
-    
-    ### Compute hashes
-    log.info('Computing hashes')
-    expe_hashes = compute_hashes(expe)
     
     ### Create output names
     oname = '{}_{}'.format(expe_file.stem, expe_hashes['global'][:6])
@@ -179,79 +186,6 @@ def compute_hashes(expe):
     expe_hashes['global'] = glob.hexdigest()
     return expe_hashes
 
-
-def compute_descriptors(expe):
-    """Compute descriptors from a standard expe recipe"""
-    script = expe['descriptors_script']
-    desc = importlib.import_module(script['name'])
-    #importlib.reload(Descriptors)
-    att = desc.run(**script['parameters'])
-    
-    return att
-
-
-def get_ground_truth(expe):
-    gt = triskele.read(expe['ground_truth'])
-    
-    # Meta labeling
-    idx_map = np.arange(gt.max() + 1)
-
-    if 'meta_labels' in expe:
-        meta_idx = pd.read_csv(expe['meta_labels'])
-        idx = np.array(meta_idx['index'])
-        midx = np.array(meta_idx['metaclass_index'])
-        idx_map[idx] = midx
-    
-    return idx_map[gt]
-
-
-def compute_classification(expe, descriptors):
-    """Read a standard expe recipe and descriptors, return the result classification"""
-    # Ground truth
-    gt = get_ground_truth(expe)
-
-    # CrossVal and ML
-    cv = expe['cross_validation']
-    cl = expe['classifier']
-
-    cross_val  = getattr(importlib.import_module(cv['package']), cv['name'])
-    classifier = getattr(importlib.import_module(cl['package']), cl['name'])
-
-    prediction = np.zeros_like(gt)
-
-    for xt, xv, yt, yv, ti in cross_val(gt, descriptors, **cv['parameters']):
-        rfc = classifier(**cl['parameters'])
-        rfc.fit(xt, yt)
-
-        ypred = rfc.predict(xv)
-
-        prediction[ti] = ypred
-        
-    return prediction
-
-
-def compute_metrics(ground_truth, classification, descriptors):
-    """Return dict of metrics for ground_truth and classification prediction in parameters"""
-    f = np.nonzero(classification)
-    pred = classification[f].ravel()
-    gt = ground_truth[f].ravel()
-    
-    results = OrderedDict() 
-    results['dimension'] = descriptors.shape[-1]
-    results['overall_accuracy'] = float(metrics.accuracy_score(gt, pred))
-    results['cohen_kappa'] = float(metrics.cohen_kappa_score(gt, pred))
-    
-    return results
-
-
-def run_metrics(expe, classification, descriptors):
-    """Compute the metrics from a standard expe recipe and an given classification"""
-    
-    ### Extensible: meta-classes
-    gt = get_ground_truth(expe)
-    return compute_metrics(gt, classification, descriptors)
-
-
 def create_report(kronos):
     expe_report = OrderedDict()
 
@@ -279,7 +213,7 @@ def main():
             log.error('Critical exception while updating work queue')
             log.error(traceback.format_exc())
             log.warning('Resuming')
-            continue
+            break # continue
         if not queue:
             watch_folder()
             continue
@@ -291,7 +225,7 @@ def main():
             log.error('Critical exception while running test. Resuming')
             log.error(traceback.format_exc())
             log.warning('Resuming')
-            continue
+            break # continue
     
 if __name__ == '__main__':
     logger.setup_logging()