WIP on refactor

minigrida/database/helpers.py

@@ -50,11 +50,11 @@ def create_session(name, desc, project_name, urgency=1):
     else:
         print('Session "{}" already exists.'.format(name))
 
-def bind_testing():
+def connect_testing():
     db.bind('sqlite', ':memory:')
     db.generate_mapping(create_tables=True)
 
-def bind(credentials_file):
+def connect(credentials_file):
     with open(credentials_file) as f:
         credentials = json.load(f)
         db.bind(**credentials)

minigrida/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]

minigrida/protocols/jurse2.py

@@ -0,0 +1,128 @@
+#!/usr/bin/env python
+# file jurse2.py
+# author Florent Guiotte <florent.guiotte@irisa.fr>
+# version 0.0
+# date 26 mai 2020
+"""Abstract
+
+doc.
+"""
+
+import importlib
+import numpy as np
+from sklearn import metrics
+import rasterio
+from .protocol import Protocol, TestError
+
+
+class Jurse2(Protocol):
+    """Second JURSE test protocol for LiDAR classification with 2D maps.
+
+    """
+
+    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._time('description')
+
+        self._log.info('Classify data')
+        try:
+            classification = self._compute_classification(descriptors)
+        except Exception:
+            raise TestError('Error occured during classification')
+        self._time('classification')
+
+        self._log.info('Run metrics')
+        metrics = self._run_metrics(classification, descriptors)
+        self._time('metrics')
+
+        cmap = str(self._results_base_name) + '.tif'
+        self._log.info('Saving classification map {}'.format(cmap))
+        triskele.write(cmap, classification)
+
+        results = OrderedDict()
+        results['classification'] = cmap
+        results['metrics'] = metrics
+        self._results = results
+
+    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, dtype=np.uint8)
+
+        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 gt_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 _get_results(self):
+        return self._results
+
+    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['dimensions'] = descriptors.shape[-1]
+        results['overall_accuracy'] = float(metrics.accuracy_score(gt, pred))
+        results['cohen_kappa'] = float(metrics.cohen_kappa_score(gt, pred))
+
+        return results

minigrida/protocols/protocol.py

@@ -10,16 +10,12 @@
 
 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._results_base_name = None
         self._log.debug('expe loaded: {}'.format(self._expe))
 
     def get_hashes(self):

minigrida/supervisor.py

@@ -3,15 +3,13 @@
 # \file supervisor.py
 # \brief TODO
 # \author Florent Guiotte <florent.guiotte@gmail.com>
-# \version 0.1
+# \version 2.1
 # \date 07 sept. 2018
 #
 # TODO details
 
-import yaml
 import importlib
-import hashlib
-from collections import OrderedDict
+import json
 import time
 import os
 import datetime
@@ -21,34 +19,10 @@ import traceback
 import logging
 import logger
 from protocols.protocol import TestError
-
-ENRICHMENT_DIR = Path('./Enrichment/')
-TEST_DIR    = ENRICHMENT_DIR / 'Tests'
-STAGING_DIR = ENRICHMENT_DIR / 'Staging'
-RESULT_DIR  = ENRICHMENT_DIR / 'Results'
-FAILED_DIR  = ENRICHMENT_DIR / 'Failed'
+import database
 
 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():
@@ -188,28 +162,12 @@ class ExpePath:
     def get_result_path(self):
         return Path(RESULT_DIR) / self._get_hash_name()
 
-    def _check_hash(self, expe):
-        if self._hash is None:
-            if 'hashes' in expe:
-                self._hash = expe['hashes']['global']
-
-    def _write(self, path, expe):
-        new_path = Path(path) / self._get_complete_name()
-        with open(new_path, 'w') as of:
-            yaml.dump(expe, of, 
-                      default_flow_style=False, 
-                      encoding=None, 
-                      allow_unicode=True)
-        self._actual.unlink()
-        self._actual = new_path
-    
-
-def watch_folder():
-    log.info('Waiting for test')
-    while not list(TEST_DIR.glob('*.yml')):
-        time.sleep(3)
+def get_database():
 
 def main():
+    print('Hello again')
+    database
+    return
     while(True):
         try:
             queue = update_queue()
@@ -239,5 +197,4 @@ if __name__ == '__main__':
     logger.setup_logging()
     log.info('Starting supervisor')
 
-    setup_yaml()
     main()