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author | 20001LastOrder <boqi.chen@mail.mcgill.ca> | 2019-07-10 10:56:00 -0400 |
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committer | 20001LastOrder <boqi.chen@mail.mcgill.ca> | 2019-07-10 10:56:00 -0400 |
commit | 991dacefdb8f78fccc359d3d2ec836dc2e7fc80a (patch) | |
tree | 6b18aa59c5f711a845aa9e3e5cf3fd3632ad7a33 /Metrics/Metrics-Calculation/metrics_plot | |
parent | add sample domain for measuring realistic metrics (diff) | |
download | VIATRA-Generator-991dacefdb8f78fccc359d3d2ec836dc2e7fc80a.tar.gz VIATRA-Generator-991dacefdb8f78fccc359d3d2ec836dc2e7fc80a.tar.zst VIATRA-Generator-991dacefdb8f78fccc359d3d2ec836dc2e7fc80a.zip |
measurements for the different violation types, comparison for differenct generation config
Diffstat (limited to 'Metrics/Metrics-Calculation/metrics_plot')
50 files changed, 98 insertions, 33 deletions
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diff --git a/Metrics/Metrics-Calculation/metrics_plot/model comparison/src/plot_ks_stats.py b/Metrics/Metrics-Calculation/metrics_plot/model comparison/src/plot_ks_stats.py index 2f39ca93..a66802d5 100644 --- a/Metrics/Metrics-Calculation/metrics_plot/model comparison/src/plot_ks_stats.py +++ b/Metrics/Metrics-Calculation/metrics_plot/model comparison/src/plot_ks_stats.py | |||
@@ -8,17 +8,19 @@ import matplotlib.pyplot as plt | |||
8 | from scipy import stats | 8 | from scipy import stats |
9 | import numpy as np | 9 | import numpy as np |
10 | from GraphType import GraphCollection | 10 | from GraphType import GraphCollection |
11 | import DistributionMetrics as metrics | ||
11 | 12 | ||
12 | def main(): | 13 | def main(): |
13 | # read models | 14 | # read models |
14 | human = GraphCollection('../input/humanOutput/', 500, 'Human') | 15 | # human = GraphCollection('../input/humanOutput/', 500, 'Human') |
15 | viatra30 = GraphCollection('../input/viatraOutput30/', 500, 'Viatra (30 nodes)') | 16 | # viatra30 = GraphCollection('../input/viatraOutput30/', 500,'Viatra (30 nodes)') |
16 | # viatra60 = GraphCollection('../input/viatraOutput60/', 500, 'Viatra (60 nodes)') | 17 | # viatra60 = GraphCollection('../input/viatraOutput60/', 500, 'Viatra (60 nodes)') |
17 | # viatra100 = GraphCollection('../input/viatraOutput100/', 500, 'Viatra (100 nodes)') | 18 | viatra100 = GraphCollection('../input/viatraOutput100/', 500, 'Viatra (100 nodes)') |
18 | # random = GraphCollection('../input/randomOutput/', 500, 'Random') | 19 | # random = GraphCollection('../input/randomOutput/', 500, 'Random') |
19 | # alloy = GraphCollection('../input/alloyOutput/', 500, 'Alloy (30 nodes)') | 20 | # alloy = GraphCollection('../input/alloyOutput/', 500, 'Alloy (30 nodes)') |
20 | 21 | realistic_viatra = GraphCollection('../input/viatra_output_consistent_100/', 50, 'Realistic Viatra With Some Constraints (100 nodes)') | |
21 | models_to_compare = [human, viatra30] | 22 | human100 = GraphCollection('../input/human_output_100/', 304, 'Human') |
23 | models_to_compare = [human100, realistic_viatra, viatra100] | ||
22 | 24 | ||
23 | # define output folder | 25 | # define output folder |
24 | outputFolder = '../output/' | 26 | outputFolder = '../output/' |
@@ -38,7 +40,7 @@ def calculateKSMatrix(dists): | |||
38 | for i in range(len(dist)): | 40 | for i in range(len(dist)): |
39 | matrix[i,i] = 0 | 41 | matrix[i,i] = 0 |
40 | for j in range(i+1, len(dist)): | 42 | for j in range(i+1, len(dist)): |
41 | value, p = stats.ks_2samp(dist[i], dist[j]) | 43 | value = metrics.euclidean_distance(dist[i], dist[j]) |
42 | matrix[i, j] = value | 44 | matrix[i, j] = value |
43 | matrix[j, i] = value | 45 | matrix[j, i] = value |
44 | return matrix | 46 | return matrix |
@@ -50,13 +52,14 @@ def calculateMDS(dissimilarities): | |||
50 | return trans | 52 | return trans |
51 | 53 | ||
52 | def plot(graphTypes, coords, title='',index = 0, savePath = ''): | 54 | def plot(graphTypes, coords, title='',index = 0, savePath = ''): |
53 | half_length = int(coords.shape[0] / len(graphTypes)) | ||
54 | color = ['blue', 'red', 'green', 'yellow'] | 55 | color = ['blue', 'red', 'green', 'yellow'] |
55 | plt.figure(index, figsize=(7, 4)) | 56 | plt.figure(index, figsize=(7, 4)) |
56 | plt.title(title) | 57 | plt.title(title) |
58 | index = 0 | ||
57 | for i in range(len(graphTypes)): | 59 | for i in range(len(graphTypes)): |
58 | x = (coords[(i*half_length):((i+1)*half_length), 0].tolist()) | 60 | x = (coords[index:index+graphTypes[i].size, 0].tolist()) |
59 | y = (coords[(i*half_length):((i+1)*half_length), 1].tolist()) | 61 | y = (coords[index:index+graphTypes[i].size, 1].tolist()) |
62 | index += graphTypes[i].size | ||
60 | plt.plot(x, y, color=color[i], marker='o', label = graphTypes[i].name, linestyle='', alpha=0.7) | 63 | plt.plot(x, y, color=color[i], marker='o', label = graphTypes[i].name, linestyle='', alpha=0.7) |
61 | plt.legend(loc='upper right') | 64 | plt.legend(loc='upper right') |
62 | plt.savefig(fname = savePath, dpi=150) | 65 | plt.savefig(fname = savePath, dpi=150) |
diff --git a/Metrics/Metrics-Calculation/metrics_plot/model_evolve_comparison/src/representative_selector .ipynb b/Metrics/Metrics-Calculation/metrics_plot/model_evolve_comparison/src/representative_selector .ipynb index 78f408fc..329a46f6 100644 --- a/Metrics/Metrics-Calculation/metrics_plot/model_evolve_comparison/src/representative_selector .ipynb +++ b/Metrics/Metrics-Calculation/metrics_plot/model_evolve_comparison/src/representative_selector .ipynb | |||
@@ -16,7 +16,7 @@ | |||
16 | }, | 16 | }, |
17 | { | 17 | { |
18 | "cell_type": "code", | 18 | "cell_type": "code", |
19 | "execution_count": 1, | 19 | "execution_count": 11, |
20 | "metadata": {}, | 20 | "metadata": {}, |
21 | "outputs": [], | 21 | "outputs": [], |
22 | "source": [ | 22 | "source": [ |
@@ -30,7 +30,8 @@ | |||
30 | "import ipywidgets as widgets\n", | 30 | "import ipywidgets as widgets\n", |
31 | "from pyclustering.cluster.kmedoids import kmedoids\n", | 31 | "from pyclustering.cluster.kmedoids import kmedoids\n", |
32 | "from pyclustering.utils.metric import distance_metric, type_metric\n", | 32 | "from pyclustering.utils.metric import distance_metric, type_metric\n", |
33 | "import random" | 33 | "import random\n", |
34 | "import numpy as np" | ||
34 | ] | 35 | ] |
35 | }, | 36 | }, |
36 | { | 37 | { |
@@ -176,23 +177,28 @@ | |||
176 | }, | 177 | }, |
177 | { | 178 | { |
178 | "cell_type": "code", | 179 | "cell_type": "code", |
179 | "execution_count": 6, | 180 | "execution_count": 15, |
180 | "metadata": {}, | 181 | "metadata": {}, |
181 | "outputs": [ | 182 | "outputs": [ |
182 | { | 183 | { |
183 | "name": "stdout", | 184 | "name": "stdout", |
184 | "output_type": "stream", | 185 | "output_type": "stream", |
185 | "text": [ | 186 | "text": [ |
186 | "0.046150929558524685\n" | 187 | "average distance: 0.04615092955852465\n", |
188 | "std: 0.017305709419913242\n", | ||
189 | "max: 0.1411706837186424\n", | ||
190 | "min: 0.0\n" | ||
187 | ] | 191 | ] |
188 | } | 192 | } |
189 | ], | 193 | ], |
190 | "source": [ | 194 | "source": [ |
191 | "total_distance = 0\n", | 195 | "distances = []\n", |
192 | "count = 0\n", | ||
193 | "for model in models:\n", | 196 | "for model in models:\n", |
194 | " total_distance += ks_value(od_rep_model.out_d, model.out_d)\n", | 197 | " distances.append(ks_value(od_rep_model.out_d, model.out_d))\n", |
195 | "print(total_distance / len(models))" | 198 | "print('average distance: ', np.mean(distances))\n", |
199 | "print('std: ', np.std(distances))\n", | ||
200 | "print('max:', max(distances))\n", | ||
201 | "print('min:', min(distances))" | ||
196 | ] | 202 | ] |
197 | }, | 203 | }, |
198 | { | 204 | { |
@@ -217,7 +223,7 @@ | |||
217 | }, | 223 | }, |
218 | { | 224 | { |
219 | "cell_type": "code", | 225 | "cell_type": "code", |
220 | "execution_count": 13, | 226 | "execution_count": 7, |
221 | "metadata": {}, | 227 | "metadata": {}, |
222 | "outputs": [ | 228 | "outputs": [ |
223 | { | 229 | { |
@@ -245,16 +251,21 @@ | |||
245 | "name": "stdout", | 251 | "name": "stdout", |
246 | "output_type": "stream", | 252 | "output_type": "stream", |
247 | "text": [ | 253 | "text": [ |
248 | "0.04679429311806747\n" | 254 | "average distance: 0.046794293118067494\n", |
255 | "std: 0.02880119213919405\n", | ||
256 | "max: 0.18702970297029703\n", | ||
257 | "min: 0.0\n" | ||
249 | ] | 258 | ] |
250 | } | 259 | } |
251 | ], | 260 | ], |
252 | "source": [ | 261 | "source": [ |
253 | "total_distance = 0\n", | 262 | "distances = []\n", |
254 | "count = 0\n", | ||
255 | "for model in models:\n", | 263 | "for model in models:\n", |
256 | " total_distance += ks_value(na_rep_model.na, model.na)\n", | 264 | " distances.append(ks_value(na_rep_model.na, model.na))\n", |
257 | "print(total_distance / len(models))" | 265 | "print('average distance: ', np.mean(distances))\n", |
266 | "print('std: ', np.std(distances))\n", | ||
267 | "print('max:', max(distances))\n", | ||
268 | "print('min:', min(distances))" | ||
258 | ] | 269 | ] |
259 | }, | 270 | }, |
260 | { | 271 | { |
@@ -279,7 +290,7 @@ | |||
279 | }, | 290 | }, |
280 | { | 291 | { |
281 | "cell_type": "code", | 292 | "cell_type": "code", |
282 | "execution_count": 16, | 293 | "execution_count": 9, |
283 | "metadata": {}, | 294 | "metadata": {}, |
284 | "outputs": [ | 295 | "outputs": [ |
285 | { | 296 | { |
@@ -300,23 +311,28 @@ | |||
300 | }, | 311 | }, |
301 | { | 312 | { |
302 | "cell_type": "code", | 313 | "cell_type": "code", |
303 | "execution_count": 18, | 314 | "execution_count": 16, |
304 | "metadata": {}, | 315 | "metadata": {}, |
305 | "outputs": [ | 316 | "outputs": [ |
306 | { | 317 | { |
307 | "name": "stdout", | 318 | "name": "stdout", |
308 | "output_type": "stream", | 319 | "output_type": "stream", |
309 | "text": [ | 320 | "text": [ |
310 | "0.07028909225833631\n" | 321 | "average distance: 0.07028909225833632\n", |
322 | "std: 0.03728189051222417\n", | ||
323 | "max: 0.21961550993809065\n", | ||
324 | "min: 0.0\n" | ||
311 | ] | 325 | ] |
312 | } | 326 | } |
313 | ], | 327 | ], |
314 | "source": [ | 328 | "source": [ |
315 | "total_distance = 0\n", | 329 | "distances = []\n", |
316 | "count = 0\n", | ||
317 | "for model in models:\n", | 330 | "for model in models:\n", |
318 | " total_distance += ks_value(mpc_rep_model.mpc, model.mpc)\n", | 331 | " distances.append(ks_value(mpc_rep_model.mpc, model.mpc))\n", |
319 | "print(total_distance / len(models))" | 332 | "print('average distance: ', np.mean(distances))\n", |
333 | "print('std: ', np.std(distances))\n", | ||
334 | "print('max:', max(distances))\n", | ||
335 | "print('min:', min(distances))" | ||
320 | ] | 336 | ] |
321 | }, | 337 | }, |
322 | { | 338 | { |
diff --git a/Metrics/Metrics-Calculation/metrics_plot/utils/DistributionMetrics.py b/Metrics/Metrics-Calculation/metrics_plot/utils/DistributionMetrics.py new file mode 100644 index 00000000..6e707108 --- /dev/null +++ b/Metrics/Metrics-Calculation/metrics_plot/utils/DistributionMetrics.py | |||
@@ -0,0 +1,43 @@ | |||
1 | from scipy import stats | ||
2 | from scipy.spatial import distance | ||
3 | |||
4 | def ks_distance(samples1, samples2): | ||
5 | value, p = stats.ks_2samp(samples1, samples2) | ||
6 | return (value, p) | ||
7 | |||
8 | def js_distance(samples1, samples2): | ||
9 | map1 = fromSamples(samples1) | ||
10 | map2 = fromSamples(samples2) | ||
11 | allKeys = set(map1.keys()) | set(map2.keys()) | ||
12 | dist1 = distributionFromMap(map1, allKeys) | ||
13 | dist2 = distributionFromMap(map2, allKeys) | ||
14 | return distance.jensenshannon(dist1, dist2, 2) | ||
15 | |||
16 | def euclidean_distance(samples1, samples2): | ||
17 | map1 = fromSamples(samples1) | ||
18 | map2 = fromSamples(samples2) | ||
19 | allKeys = set(map1.keys()) | set(map2.keys()) | ||
20 | dist1 = distributionFromMap(map1, allKeys) | ||
21 | dist2 = distributionFromMap(map2, allKeys) | ||
22 | distance = 0 | ||
23 | for i in range(len(dist2)): | ||
24 | distance += pow(dist1[i] - dist2[i], 2) | ||
25 | return pow(distance, 0.5) | ||
26 | |||
27 | def fromSamples(samples): | ||
28 | m = {} | ||
29 | length = len(samples) | ||
30 | for sample in samples: | ||
31 | value = m.get(sample, 0) | ||
32 | m[sample] = value + 1 | ||
33 | for key in list(m.keys()): | ||
34 | m[key] /= length | ||
35 | return m | ||
36 | |||
37 | def distributionFromMap(m, allKeys): | ||
38 | dist = [] | ||
39 | for key in allKeys: | ||
40 | value = m.get(key, 0) | ||
41 | dist.append(value) | ||
42 | return dist | ||
43 | |||
diff --git a/Metrics/Metrics-Calculation/metrics_plot/utils/GraphType.py b/Metrics/Metrics-Calculation/metrics_plot/utils/GraphType.py index 13754e80..827c2a5e 100644 --- a/Metrics/Metrics-Calculation/metrics_plot/utils/GraphType.py +++ b/Metrics/Metrics-Calculation/metrics_plot/utils/GraphType.py | |||
@@ -11,13 +11,13 @@ class GraphCollection: | |||
11 | self.nas = [] | 11 | self.nas = [] |
12 | self.mpcs = [] | 12 | self.mpcs = [] |
13 | self.name = name | 13 | self.name = name |
14 | self.size = number | ||
14 | models = reader.readmultiplefiles(path, number, shouldShuffle) | 15 | models = reader.readmultiplefiles(path, number, shouldShuffle) |
15 | for i in range(len(models)): | 16 | for i in range(len(models)): |
16 | contents, out_d, na, mpc = reader.getmetrics(models[i]) | 17 | contents, out_d, na, mpc = reader.getmetrics(models[i]) |
17 | self.out_ds.append(out_d) | 18 | self.out_ds.append(out_d) |
18 | self.nas.append(na) | 19 | self.nas.append(na) |
19 | self.mpcs.append(mpc) | 20 | self.mpcs.append(mpc) |
20 | print(len(self.out_ds)) | ||
21 | 21 | ||
22 | #Graph stat for one graph | 22 | #Graph stat for one graph |
23 | class GraphStat: | 23 | class GraphStat: |
diff --git a/Metrics/Metrics-Calculation/metrics_plot/utils/readCSV.py b/Metrics/Metrics-Calculation/metrics_plot/utils/readCSV.py index e0402519..b27a0ffc 100644 --- a/Metrics/Metrics-Calculation/metrics_plot/utils/readCSV.py +++ b/Metrics/Metrics-Calculation/metrics_plot/utils/readCSV.py | |||
@@ -24,9 +24,12 @@ def readcsvfile(filename): | |||
24 | # meta models are string | 24 | # meta models are string |
25 | elif(arr[0] == constants.METAMODEL): | 25 | elif(arr[0] == constants.METAMODEL): |
26 | contents[constants.METAMODEL] = arr[1:] | 26 | contents[constants.METAMODEL] = arr[1:] |
27 | # all other contants are integer | 27 | # NA and OD are integers |
28 | else: | 28 | else: |
29 | contents[arr[0]] = list(map(int, arr[1:])) | 29 | try: |
30 | contents[arr[0]] = list(map(int, arr[1:])) | ||
31 | except: | ||
32 | print(arr[0], ' is not integer') | ||
30 | f.close() | 33 | f.close() |
31 | return contents | 34 | return contents |
32 | 35 | ||