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updated to semantic class branch
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‎panoptica/example_spine_matched_instance.ipynb‎

Lines changed: 21 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -61,7 +61,7 @@
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"import numpy as np\n",
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"from auxiliary.nifti.io import read_nifti\n",
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"from rich import print as pprint\n",
64-
"from panoptica import MatchedInstancePair, Panoptic_Evaluator\n",
64+
"from panoptica import MatchedInstancePair, Panoptica_Evaluator\n",
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"from panoptica.metrics import Metric"
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]
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},
@@ -191,21 +191,20 @@
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"output_type": "stream",
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"text": [
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"Panoptic: Start Evaluation\n",
194-
"-- Got MatchedInstancePair, will evaluate instances\n",
195-
"-- evaluate took 2.0301928520202637 seconds to execute.\n"
194+
"-- Got MatchedInstancePair, will evaluate instances\n"
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]
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}
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],
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"source": [
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"sample = MatchedInstancePair(prediction_arr=pred_masks, reference_arr=ref_masks)\n",
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"\n",
202-
"evaluator = Panoptic_Evaluator(\n",
201+
"evaluator = Panoptica_Evaluator(\n",
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" expected_input=MatchedInstancePair,\n",
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" decision_metric=Metric.IOU,\n",
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" decision_threshold=0.5,\n",
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")\n",
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"\n",
208-
"result, debug_data = evaluator.evaluate(sample)"
207+
"result, debug_data = evaluator.evaluate(sample)[\"ungrouped\"]"
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]
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},
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{
@@ -237,13 +236,16 @@
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"+++ GLOBAL +++\n",
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"Global Binary Dice (global_bin_dsc): 0.9744370224078394\n",
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"Global Binary Centerline Dice (global_bin_cldsc): 0.9637064011802574\n",
239+
"Global Binary Average Symmetric Surface Distance (global_bin_assd): 0.1499152780072207\n",
240+
"Global Binary Relative Volume Difference (global_bin_rvd): -0.0006011763989268869\n",
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"\n",
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"+++ INSTANCE +++\n",
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"Segmentation Quality IoU (sq): 0.8328184295330796 +- 0.15186064004517466\n",
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"Panoptic Quality IoU (pq): 0.8328184295330796\n",
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"Segmentation Quality Dsc (sq_dsc): 0.900292616009954 +- 0.10253566174957332\n",
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"Panoptic Quality Dsc (pq_dsc): 0.900292616009954\n",
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"Segmentation Quality Assd (sq_assd): 0.250331887879225 +- 0.07696680402317076\n",
248+
"Segmentation Quality Relative Volume Difference (sq_rvd): 0.0028133049062930553 +- 0.034518928495505724\n",
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"\n"
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]
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}
@@ -292,17 +294,23 @@
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" <span style=\"color: #008000; text-decoration-color: #008000\">'tp'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">22</span>,\n",
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" <span style=\"color: #008000; text-decoration-color: #008000\">'fp'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0</span>,\n",
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" <span style=\"color: #008000; text-decoration-color: #008000\">'fn'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0</span>,\n",
297+
" <span style=\"color: #008000; text-decoration-color: #008000\">'prec'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">1.0</span>,\n",
298+
" <span style=\"color: #008000; text-decoration-color: #008000\">'rec'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">1.0</span>,\n",
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" <span style=\"color: #008000; text-decoration-color: #008000\">'rq'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">1.0</span>,\n",
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" <span style=\"color: #008000; text-decoration-color: #008000\">'global_bin_dsc'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.9744370224078394</span>,\n",
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" <span style=\"color: #008000; text-decoration-color: #008000\">'global_bin_cldsc'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.9637064011802574</span>,\n",
302+
" <span style=\"color: #008000; text-decoration-color: #008000\">'global_bin_assd'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.1499152780072207</span>,\n",
303+
" <span style=\"color: #008000; text-decoration-color: #008000\">'global_bin_rvd'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">-0.0006011763989268869</span>,\n",
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" <span style=\"color: #008000; text-decoration-color: #008000\">'sq'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.8328184295330796</span>,\n",
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" <span style=\"color: #008000; text-decoration-color: #008000\">'sq_std'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.15186064004517466</span>,\n",
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" <span style=\"color: #008000; text-decoration-color: #008000\">'pq'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.8328184295330796</span>,\n",
301307
" <span style=\"color: #008000; text-decoration-color: #008000\">'sq_dsc'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.900292616009954</span>,\n",
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" <span style=\"color: #008000; text-decoration-color: #008000\">'sq_dsc_std'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.10253566174957332</span>,\n",
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" <span style=\"color: #008000; text-decoration-color: #008000\">'pq_dsc'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.900292616009954</span>,\n",
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" <span style=\"color: #008000; text-decoration-color: #008000\">'sq_assd'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.250331887879225</span>,\n",
305-
" <span style=\"color: #008000; text-decoration-color: #008000\">'sq_assd_std'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.07696680402317076</span>\n",
311+
" <span style=\"color: #008000; text-decoration-color: #008000\">'sq_assd_std'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.07696680402317076</span>,\n",
312+
" <span style=\"color: #008000; text-decoration-color: #008000\">'sq_rvd'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.0028133049062930553</span>,\n",
313+
" <span style=\"color: #008000; text-decoration-color: #008000\">'sq_rvd_std'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.034518928495505724</span>\n",
306314
"<span style=\"font-weight: bold\">}</span>\n",
307315
"</pre>\n"
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],
@@ -314,17 +322,23 @@
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" \u001b[32m'tp'\u001b[0m: \u001b[1;36m22\u001b[0m,\n",
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" \u001b[32m'fp'\u001b[0m: \u001b[1;36m0\u001b[0m,\n",
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" \u001b[32m'fn'\u001b[0m: \u001b[1;36m0\u001b[0m,\n",
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" \u001b[32m'prec'\u001b[0m: \u001b[1;36m1.0\u001b[0m,\n",
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" \u001b[32m'rec'\u001b[0m: \u001b[1;36m1.0\u001b[0m,\n",
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" \u001b[32m'rq'\u001b[0m: \u001b[1;36m1.0\u001b[0m,\n",
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" \u001b[32m'global_bin_dsc'\u001b[0m: \u001b[1;36m0.9744370224078394\u001b[0m,\n",
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" \u001b[32m'global_bin_cldsc'\u001b[0m: \u001b[1;36m0.9637064011802574\u001b[0m,\n",
330+
" \u001b[32m'global_bin_assd'\u001b[0m: \u001b[1;36m0.1499152780072207\u001b[0m,\n",
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" \u001b[32m'global_bin_rvd'\u001b[0m: \u001b[1;36m-0.0006011763989268869\u001b[0m,\n",
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" \u001b[32m'sq'\u001b[0m: \u001b[1;36m0.8328184295330796\u001b[0m,\n",
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" \u001b[32m'sq_std'\u001b[0m: \u001b[1;36m0.15186064004517466\u001b[0m,\n",
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" \u001b[32m'pq'\u001b[0m: \u001b[1;36m0.8328184295330796\u001b[0m,\n",
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" \u001b[32m'sq_dsc'\u001b[0m: \u001b[1;36m0.900292616009954\u001b[0m,\n",
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" \u001b[32m'sq_dsc_std'\u001b[0m: \u001b[1;36m0.10253566174957332\u001b[0m,\n",
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" \u001b[32m'pq_dsc'\u001b[0m: \u001b[1;36m0.900292616009954\u001b[0m,\n",
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" \u001b[32m'sq_assd'\u001b[0m: \u001b[1;36m0.250331887879225\u001b[0m,\n",
327-
" \u001b[32m'sq_assd_std'\u001b[0m: \u001b[1;36m0.07696680402317076\u001b[0m\n",
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" \u001b[32m'sq_assd_std'\u001b[0m: \u001b[1;36m0.07696680402317076\u001b[0m,\n",
340+
" \u001b[32m'sq_rvd'\u001b[0m: \u001b[1;36m0.0028133049062930553\u001b[0m,\n",
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" \u001b[32m'sq_rvd_std'\u001b[0m: \u001b[1;36m0.034518928495505724\u001b[0m\n",
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"\u001b[1m}\u001b[0m\n"
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]
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},

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