Supervisor and Jurse passing tests

.gitignore

@@ -1,3 +1,4 @@
 Enrichment/
 __pycache__/
 Logs/
+[Dd]ata/

descriptors/dfc_aps.py

@@ -0,0 +1,30 @@
+import numpy as np
+import yaml
+
+import sys
+sys.path.append('..')
+import ld2dap
+
+def run(rasters, treshold=1e4, areas=None, sd=None, moi=None):
+    # Parse attribute type
+    treshold = float(treshold)
+    areas = None if areas is None else np.array(areas).astype(np.float).astype(np.int)
+    sd = None if sd is None else np.array(sd).astype(np.float)
+    moi = None if moi is None else np.array(moi).astype(np.float)
+
+    # APs Pipelines
+    loader = ld2dap.LoadTIFF(rasters)
+    dfc_filter = ld2dap.Treshold(treshold)
+    dfc_filter.input = loader
+    aps = ld2dap.AttributeProfiles(area=areas, sd=sd, moi=moi)
+    aps.input = dfc_filter
+    out_vectors = ld2dap.RawOutput()
+    out_vectors.input = aps
+
+    # Compute vectors
+    out_vectors.run()
+    
+    return out_vectors.data
+
+def version():
+    return 'v0.0'

descriptors/dfc_base.py

@@ -0,0 +1,34 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# \file dfc_base.py
+# \brief TODO
+# \author Florent Guiotte <florent.guiotte@gmail.com>
+# \version 0.1
+# \date 27 août 2018
+#
+# TODO details
+
+import numpy as np
+
+import sys
+sys.path.append('..')
+import ld2dap
+
+def run(rasters, treshold=1e4):
+    # Parse parameters type
+    treshold = float(treshold)
+
+    # Pipelines
+    loader = ld2dap.LoadTIFF(rasters)
+    dfc_filter = ld2dap.Treshold(treshold)
+    dfc_filter.input = loader
+    out_vectors = ld2dap.RawOutput()
+    out_vectors.input = dfc_filter
+
+    # Compute vectors
+    out_vectors.run()
+
+    return out_vectors.data
+
+def version():
+    return 'v0.0'

descriptors/dfc_daps.py

@@ -0,0 +1,41 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# \file dfc_daps.py
+# \brief TODO
+# \author Florent Guiotte <florent.guiotte@gmail.com>
+# \version 0.1
+# \date 27 août 2018
+#
+# TODO details
+
+import numpy as np
+
+import sys
+sys.path.append('..')
+import ld2dap
+
+def run(rasters, treshold=1e4, areas=None, sd=None, moi=None):
+    # Parse parameters type
+    treshold = float(treshold)
+    areas = None if areas is None else np.array(areas).astype(np.float).astype(np.int)
+    sd = None if sd is None else np.array(sd).astype(np.float)
+    moi = None if moi is None else np.array(moi).astype(np.float)
+
+    # Pipelines
+    loader = ld2dap.LoadTIFF(rasters)
+    dfc_filter = ld2dap.Treshold(treshold)
+    dfc_filter.input = loader
+    aps = ld2dap.AttributeProfiles(area=areas, sd=sd, moi=moi)
+    aps.input = dfc_filter
+    differential = ld2dap.Differential()
+    differential.input = aps
+    out_vectors = ld2dap.RawOutput()
+    out_vectors.input = differential
+
+    # Compute vectors
+    out_vectors.run()
+
+    return out_vectors.data
+
+def version():
+    return 'v0.0'

descriptors/dfc_dsdaps.py

@@ -0,0 +1,41 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# \file dfc_dsdaps.py
+# \brief TODO
+# \author Florent Guiotte <florent.guiotte@gmail.com>
+# \version 0.1
+# \date 28 août 2018
+#
+# TODO details
+
+import numpy as np
+
+import sys
+sys.path.append('..')
+import ld2dap
+
+def run(rasters, treshold=1e4, areas=None, sd=None, moi=None):
+    # Parse parameters type
+    treshold = float(treshold)
+    areas = None if areas is None else np.array(areas).astype(np.float).astype(np.int)
+    sd = None if sd is None else np.array(sd).astype(np.float)
+    moi = None if moi is None else np.array(moi).astype(np.float)
+
+    # Pipelines
+    loader = ld2dap.LoadTIFF(rasters)
+    dfc_filter = ld2dap.Treshold(treshold)
+    dfc_filter.input = loader
+    sdaps = ld2dap.SelfDualAttributeProfiles(area=areas, sd=sd, moi=moi)
+    sdaps.input = dfc_filter
+    differential = ld2dap.Differential()
+    differential.input = sdaps
+    out_vectors = ld2dap.RawOutput()
+    out_vectors.input = differential
+
+    # Compute vectors
+    out_vectors.run()
+
+    return out_vectors.data
+
+def version():
+    return 'v0.0'

descriptors/dfc_lfaps.py

@@ -0,0 +1,57 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# \file dfc_lfaps.py
+# \brief TODO
+# \author Florent Guiotte <florent.guiotte@gmail.com>
+# \version 0.1
+# \date 27 août 2018
+#
+# TODO details
+
+import numpy as np
+
+import sys
+sys.path.append('..')
+import ld2dap
+
+# TODO: Add param percentile?
+
+dispatcher = {
+        'mean': np.mean, # Arithmetic mean
+        'median': np.median, # Median
+        'average': np.average, # Weighted average (=mean ?)
+        'std': np.std, # Standard deviation
+        'var': np.var, # Variance
+        'amax': np.amax, # Maximum
+        'amin': np.amin, # Minimum
+        'ptp': np.ptp, # Range of values (max - min)
+        }
+
+def run(rasters, treshold=1e4, areas=None, sd=None, moi=None, features=['mean'], patch_size=3):
+    # Parse parameters type
+    treshold = float(treshold)
+    areas = None if areas is None else np.array(areas).astype(np.float).astype(np.int)
+    sd = None if sd is None else np.array(sd).astype(np.float)
+    moi = None if moi is None else np.array(moi).astype(np.float)
+    patch_size = int(patch_size)
+    features = [dispatcher[x] for x in features]
+
+    # Pipelines
+    loader = ld2dap.LoadTIFF(rasters)
+    dfc_filter = ld2dap.Treshold(treshold)
+    dfc_filter.input = loader
+    aps = ld2dap.AttributeProfiles(area=areas, sd=sd, moi=moi)
+    aps.input = dfc_filter
+    local_features = ld2dap.LocalFeatures(features, patch_size)
+    local_features.input = aps
+    out_vectors = ld2dap.RawOutput()
+    out_vectors.input = local_features
+
+    # Compute vectors
+    out_vectors.run()
+
+    return out_vectors.data
+
+def version():
+    return 'v0.0'
+

descriptors/dfc_lfsdaps.py

@@ -0,0 +1,57 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# \file dfc_lfsdaps.py
+# \brief TODO
+# \author Florent Guiotte <florent.guiotte@gmail.com>
+# \version 0.1
+# \date 28 août 2018
+#
+# TODO details
+
+import numpy as np
+
+import sys
+sys.path.append('..')
+import ld2dap
+
+# TODO: Add param percentile?
+
+dispatcher = {
+        'mean': np.mean, # Arithmetic mean
+        'median': np.median, # Median
+        'average': np.average, # Weighted average (=mean ?)
+        'std': np.std, # Standard deviation
+        'var': np.var, # Variance
+        'amax': np.amax, # Maximum
+        'amin': np.amin, # Minimum
+        'ptp': np.ptp, # Range of values (max - min)
+        }
+
+def run(rasters, treshold=1e4, areas=None, sd=None, moi=None, features=['mean'], patch_size=3):
+    # Parse parameters type
+    treshold = float(treshold)
+    areas = None if areas is None else np.array(areas).astype(np.float).astype(np.int)
+    sd = None if sd is None else np.array(sd).astype(np.float)
+    moi = None if moi is None else np.array(moi).astype(np.float)
+    patch_size = int(patch_size)
+    features = [dispatcher[x] for x in features]
+
+    # Pipelines
+    loader = ld2dap.LoadTIFF(rasters)
+    dfc_filter = ld2dap.Treshold(treshold)
+    dfc_filter.input = loader
+    sdaps = ld2dap.SelfDualAttributeProfiles(area=areas, sd=sd, moi=moi)
+    sdaps.input = dfc_filter
+    local_features = ld2dap.LocalFeatures(features, patch_size)
+    local_features.input = sdaps
+    out_vectors = ld2dap.RawOutput()
+    out_vectors.input = local_features
+
+    # Compute vectors
+    out_vectors.run()
+
+    return out_vectors.data
+
+def version():
+    return 'v0.0'
+

descriptors/dfc_sdaps.py

@@ -0,0 +1,40 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# \file dfc_sdaps.py
+# \brief TODO
+# \author Florent Guiotte <florent.guiotte@gmail.com>
+# \version 0.1
+# \date 27 août 2018
+#
+# TODO details
+
+import numpy as np
+
+import sys
+sys.path.append('..')
+import ld2dap
+
+def run(rasters, treshold=1e4, areas=None, sd=None, moi=None):
+    # Parse parameters type
+    treshold = float(treshold)
+    areas = None if areas is None else np.array(areas).astype(np.float).astype(np.int)
+    sd = None if sd is None else np.array(sd).astype(np.float)
+    moi = None if moi is None else np.array(moi).astype(np.float)
+
+    # Pipelines
+    loader = ld2dap.LoadTIFF(rasters)
+    dfc_filter = ld2dap.Treshold(treshold)
+    dfc_filter.input = loader
+    sdaps = ld2dap.SelfDualAttributeProfiles(area=areas, sd=sd, moi=moi)
+    sdaps.input = dfc_filter
+    out_vectors = ld2dap.RawOutput()
+    out_vectors.input = sdaps
+
+    # Compute vectors
+    out_vectors.run()
+
+    return out_vectors.data
+
+def version():
+    return 'v0.0'
+

protocols/jurse.py

@@ -14,9 +14,6 @@ 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
 
@@ -51,15 +48,27 @@ class Jurse(Protocol):
             descriptors = self._compute_descriptors()
         except Exception:
             raise TestError('Error occured during description')
+        self._time('description')
 
         self._log.info('Classify data')
         try:
-            classification = self._compute_classificatin(descriptors)
+            classification = self._compute_classification(descriptors)
         except Exception:
             raise TestError('Error occured during classification')
+        self._time('classification')
 
         self._log.info('Run metrics')
-        self._metrics = self._run_metrics(classification, descriptors)
+        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']
@@ -80,7 +89,7 @@ class Jurse(Protocol):
         cross_val = getattr(importlib.import_module(cv['package']), cv['name'])
         classifier = getattr(importlib.import_module(cl['package']), cl['name'])
 
-        prediction = np.zeros_like(gt)
+        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'])
@@ -99,7 +108,7 @@ class Jurse(Protocol):
         # Meta labeling
         idx_map = np.arange(gt.max() + 1)
 
-        if 'meta_labels' in self._expe:
+        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'])
@@ -107,6 +116,9 @@ class Jurse(Protocol):
 
         return idx_map[gt]
 
+    def _get_results(self):
+        return self._results
+
     def _run_metrics(self, classification, descriptors):
         gt = self._get_ground_truth()
 
@@ -115,7 +127,7 @@ class Jurse(Protocol):
         gt = gt[f].ravel()
 
         results = OrderedDict()
-        results['dimension'] = descriptors.shape[-1]
+        results['dimensions'] = descriptors.shape[-1]
         results['overall_accuracy'] = float(metrics.accuracy_score(gt, pred))
         results['cohen_kappa'] = float(metrics.cohen_kappa_score(gt, pred))
 

protocols/protocol.py

@@ -19,22 +19,25 @@ class Protocol:
         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):
         self._log.info('Computing hashes')
         return(self._get_hashes())
 
+    def set_results_base_name(self, base_name):
+        self._results_base_name = base_name
+
     def run(self):
         self._pt = time.process_time()
         self._run()
-# TODO: Strop process timer
 
     def get_results(self):
-        self._get_results()
+        return self._get_results()
 
     def get_process_time(self):
-        return self._times()
+        return self._times
 
     def _time(self, process):
         self._times[process] = time.process_time() - self._pt

result_mockup.yml

@@ -13,10 +13,9 @@ protocol:
 expe:
   ground_truth: 
     raster: ./Data/ground_truth/2018_IEEE_GRSS_DFC_GT_TR.tif
-    meta_labels: ./Data/ground_truth/jurse_idx.csv
+    meta_labels: ./Data/ground_truth/jurse_meta_idx.csv
   descriptors_script:
-    name: dfc_aps
-    package: descriptors
+    name: descriptors.dfc_aps
     parameters:
       areas:
       - 100
@@ -25,8 +24,8 @@ expe:
       - 0.5
       - 0.9
       rasters:
-      - ./Data/phase1_rasters/DEM+B_C123/UH17_GEM051_TR.tif
-      - ./Data/phase1_rasters/DEM_C123_3msr/UH17_GEG051_TR.tif
+      - ./Data/dfc_rasters/DEM+B_C123/UH17_GEM051_TR.tif
+      - ./Data/dfc_rasters/DEM_C123_3msr/UH17_GEG051_TR.tif
       treshold: 1e4
   cross_validation:
     name: APsCVG

supervisor.py

@@ -76,8 +76,10 @@ def run(expe_file):
 
     ### Load protocol
     try:
-        protocol = getattr(importlib.import_module(test['protocol']['package']),
-                           test['protocol']['name'])
+        #protocol = getattr(importlib.import_module(test['protocol']['package']), test['protocol']['name'])
+        protocol_module = importlib.import_module(test['protocol']['package'])
+        importlib.reload(protocol_module)
+        protocol = getattr(protocol_module, test['protocol']['name'])
         experience = protocol(test['expe'])
     except Exception as e:
         err = 'Could not load protocol from test {}'.format(expe_file)
@@ -91,6 +93,8 @@ def run(expe_file):
     test['report'] = create_report(start_time)
     expe_file.stage(test)
 
+    experience.set_results_base_name(expe_file.get_result_path())
+
     ### Run test
     try:
         experience.run()
@@ -105,15 +109,14 @@ def run(expe_file):
     ### Write complete report
     report = create_report(start_time, end_time)
     ressources = OrderedDict()
-    ressouces['ram'] = None
-    ressouces['proccess_time'] = experience.get_process_time()
-    report['ressources'] = ressouces
+    ressources['ram'] = None
+    ressources['proccess_time'] = experience.get_process_time()
+    report['ressources'] = ressources
     test['report'] = report
 
     ### Write results
     test['results'] = experience.get_results()
     expe_file.result(test)
-    log.info('Additional results in {}'.format(expe_file.get_result_path()))
 
     ### End of test
     log.info('Test complete')
@@ -274,7 +277,7 @@ def create_report(stime=None, etime=None):
 def watch_folder():
     log.info('Waiting for test')
     while not list(TEST_DIR.glob('*.yml')):
-        time.sleep(10)
+        time.sleep(3)
 
 class Kronos(object):
     def __init__(self):

test_mockup.yml

@@ -13,10 +13,9 @@ protocol:
 expe:
   ground_truth: 
     raster: ./Data/ground_truth/2018_IEEE_GRSS_DFC_GT_TR.tif
-    meta_labels: ./Data/ground_truth/jurse_idx.csv
+    meta_labels: ./Data/ground_truth/jurse_meta_idx.csv
   descriptors_script:
-    name: dfc_aps
-    package: descriptors
+    name: descriptors.dfc_aps
     parameters:
       areas:
       - 100
@@ -25,8 +24,8 @@ expe:
       - 0.5
       - 0.9
       rasters:
-      - ./Data/phase1_rasters/DEM+B_C123/UH17_GEM051_TR.tif
-      - ./Data/phase1_rasters/DEM_C123_3msr/UH17_GEG051_TR.tif
+      - ./Data/dfc_rasters/DEM+B_C123/UH17_GEM051_TR.tif
+      - ./Data/dfc_rasters/DEM_C123_3msr/UH17_GEG051_TR.tif
       treshold: 1e4
   cross_validation:
     name: APsCVG
@@ -38,6 +37,6 @@ expe:
     package: sklearn.ensemble
     parameters:
       min_samples_leaf: 10
-      n_estimators: 50
+      n_estimators: 10
       n_jobs: -1
       random_state: 0