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Merged
Hendrik-code merged 1 commit into from
Jan 15, 2024
Merged

updated tutorials to modular_metrics PR #12

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52 changes: 27 additions & 25 deletions panoptica/example_spine_matched_instance.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,8 @@
"import numpy as np\n",
"from auxiliary.nifti.io import read_nifti\n",
"from rich import print as pprint\n",
"from panoptica import MatchedInstancePair, Panoptic_Evaluator"
"from panoptica import MatchedInstancePair, Panoptic_Evaluator\n",
"from panoptica.metrics import Metrics"
]
},
{
Expand Down Expand Up @@ -192,7 +193,7 @@
"text": [
"Panoptic: Start Evaluation\n",
"-- Got MatchedInstancePair, will evaluate instances\n",
"-- evaluate took 1.7750227451324463 seconds to execute.\n"
"-- evaluate took 1.4501242637634277 seconds to execute.\n"
]
}
],
Expand All @@ -201,7 +202,8 @@
"\n",
"evaluator = Panoptic_Evaluator(\n",
" expected_input=MatchedInstancePair,\n",
" iou_threshold=0.5,\n",
" decision_metric=Metrics.IOU,\n",
" decision_threshold=0.5,\n",
")\n",
"\n",
"result, debug_data = evaluator.evaluate(sample)"
Expand All @@ -226,15 +228,15 @@
"text": [
"Number of instances in prediction: 22\n",
"Number of instances in reference: 22\n",
"True Positives (tp): 19\n",
"False Positives (fp): 3\n",
"False Negatives (fn): 3\n",
"Recognition Quality / F1 Score (RQ): 0.8636363636363636\n",
"Segmentation Quality (SQ): 0.8328184295330796 ± 0.15186064004517466\n",
"True Positives (tp): 22\n",
"False Positives (fp): 0\n",
"False Negatives (fn): 0\n",
"Recognition Quality / F1 Score (RQ): 1.0\n",
"Segmentation Quality (SQ): 0.719252280051296 ± 0.15186064004517466\n",
"Panoptic Quality (PQ): 0.719252280051296\n",
"DSC-based Segmentation Quality (DQ_DSC): 0.900292616009954 ± 0.10253566174957332\n",
"DSC-based Segmentation Quality (DQ_DSC): 0.7775254410995057 ± 0.10253566174957332\n",
"DSC-based Panoptic Quality (PQ_DSC): 0.7775254410995057\n",
"Average symmetric surface distance (ASSD): 0.250331887879225 ± 0.07696680402317076\n",
"Average symmetric surface distance (ASSD): 0.2161957213502398 ± 0.07696680402317076\n",
"ASSD-based Panoptic Quality (PQ_ASSD): 0.2161957213502398\n"
]
}
Expand Down Expand Up @@ -280,17 +282,17 @@
"<span style=\"font-weight: bold\">{</span>\n",
" <span style=\"color: #008000; text-decoration-color: #008000\">'num_pred_instances'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">22</span>,\n",
" <span style=\"color: #008000; text-decoration-color: #008000\">'num_ref_instances'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">22</span>,\n",
" <span style=\"color: #008000; text-decoration-color: #008000\">'tp'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">19</span>,\n",
" <span style=\"color: #008000; text-decoration-color: #008000\">'fp'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">3</span>,\n",
" <span style=\"color: #008000; text-decoration-color: #008000\">'fn'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">3</span>,\n",
" <span style=\"color: #008000; text-decoration-color: #008000\">'rq'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.8636363636363636</span>,\n",
" <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",
" <span style=\"color: #008000; text-decoration-color: #008000\">'tp'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">22</span>,\n",
" <span style=\"color: #008000; text-decoration-color: #008000\">'fp'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0</span>,\n",
" <span style=\"color: #008000; text-decoration-color: #008000\">'fn'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0</span>,\n",
" <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",
" <span style=\"color: #008000; text-decoration-color: #008000\">'sq'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.719252280051296</span>,\n",
" <span style=\"color: #008000; text-decoration-color: #008000\">'sq_sd'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.15186064004517466</span>,\n",
" <span style=\"color: #008000; text-decoration-color: #008000\">'pq'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.719252280051296</span>,\n",
" <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",
" <span style=\"color: #008000; text-decoration-color: #008000\">'sq_dsc'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.7775254410995057</span>,\n",
" <span style=\"color: #008000; text-decoration-color: #008000\">'sq_dsc_sd'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.10253566174957332</span>,\n",
" <span style=\"color: #008000; text-decoration-color: #008000\">'pq_dsc'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.7775254410995057</span>,\n",
" <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",
" <span style=\"color: #008000; text-decoration-color: #008000\">'sq_assd'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.2161957213502398</span>,\n",
" <span style=\"color: #008000; text-decoration-color: #008000\">'sq_assd_sd'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.07696680402317076</span>,\n",
" <span style=\"color: #008000; text-decoration-color: #008000\">'pq_assd'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.2161957213502398</span>\n",
"<span style=\"font-weight: bold\">}</span>\n",
Expand All @@ -301,17 +303,17 @@
"\u001b[1m{\u001b[0m\n",
" \u001b[32m'num_pred_instances'\u001b[0m: \u001b[1;36m22\u001b[0m,\n",
" \u001b[32m'num_ref_instances'\u001b[0m: \u001b[1;36m22\u001b[0m,\n",
" \u001b[32m'tp'\u001b[0m: \u001b[1;36m19\u001b[0m,\n",
" \u001b[32m'fp'\u001b[0m: \u001b[1;36m3\u001b[0m,\n",
" \u001b[32m'fn'\u001b[0m: \u001b[1;36m3\u001b[0m,\n",
" \u001b[32m'rq'\u001b[0m: \u001b[1;36m0.8636363636363636\u001b[0m,\n",
" \u001b[32m'sq'\u001b[0m: \u001b[1;36m0.8328184295330796\u001b[0m,\n",
" \u001b[32m'tp'\u001b[0m: \u001b[1;36m22\u001b[0m,\n",
" \u001b[32m'fp'\u001b[0m: \u001b[1;36m0\u001b[0m,\n",
" \u001b[32m'fn'\u001b[0m: \u001b[1;36m0\u001b[0m,\n",
" \u001b[32m'rq'\u001b[0m: \u001b[1;36m1.0\u001b[0m,\n",
" \u001b[32m'sq'\u001b[0m: \u001b[1;36m0.719252280051296\u001b[0m,\n",
" \u001b[32m'sq_sd'\u001b[0m: \u001b[1;36m0.15186064004517466\u001b[0m,\n",
" \u001b[32m'pq'\u001b[0m: \u001b[1;36m0.719252280051296\u001b[0m,\n",
" \u001b[32m'sq_dsc'\u001b[0m: \u001b[1;36m0.900292616009954\u001b[0m,\n",
" \u001b[32m'sq_dsc'\u001b[0m: \u001b[1;36m0.7775254410995057\u001b[0m,\n",
" \u001b[32m'sq_dsc_sd'\u001b[0m: \u001b[1;36m0.10253566174957332\u001b[0m,\n",
" \u001b[32m'pq_dsc'\u001b[0m: \u001b[1;36m0.7775254410995057\u001b[0m,\n",
" \u001b[32m'sq_assd'\u001b[0m: \u001b[1;36m0.250331887879225\u001b[0m,\n",
" \u001b[32m'sq_assd'\u001b[0m: \u001b[1;36m0.2161957213502398\u001b[0m,\n",
" \u001b[32m'sq_assd_sd'\u001b[0m: \u001b[1;36m0.07696680402317076\u001b[0m,\n",
" \u001b[32m'pq_assd'\u001b[0m: \u001b[1;36m0.2161957213502398\u001b[0m\n",
"\u001b[1m}\u001b[0m\n"
Expand Down Expand Up @@ -343,7 +345,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.13"
"version": "3.11.6"
}
},
"nbformat": 4,
Expand Down
24 changes: 15 additions & 9 deletions panoptica/example_spine_semantic.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -88,7 +88,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -105,7 +105,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 14,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -181,7 +181,7 @@
"-- Got SemanticPair, will approximate instances\n",
"-- Got UnmatchedInstancePair, will match instances\n",
"-- Got MatchedInstancePair, will evaluate instances\n",
"-- evaluate took 4.660651922225952 seconds to execute.\n"
"-- evaluate took 3.744478940963745 seconds to execute.\n"
]
}
],
Expand All @@ -192,7 +192,6 @@
" expected_input=SemanticPair,\n",
" instance_approximator=ConnectedComponentsInstanceApproximator(),\n",
" instance_matcher=NaiveThresholdMatching(),\n",
" iou_threshold=0.5,\n",
")\n",
"\n",
"result, debug_data = evaluator.evaluate(sample)"
Expand All @@ -208,7 +207,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 16,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -237,7 +236,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 17,
"metadata": {},
"outputs": [
{
Expand All @@ -261,7 +260,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 18,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -316,6 +315,13 @@
"# get dict for further processing, e.g. for pandas\n",
"pprint(\"results dict: \", result.to_dict())"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -334,7 +340,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.13"
"version": "3.11.6"
}
},
"nbformat": 4,
Expand Down
26 changes: 16 additions & 10 deletions panoptica/example_spine_unmatched_instance.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -84,7 +84,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 2,
"metadata": {},
"outputs": [
{
Expand All @@ -96,7 +96,7 @@
" 107, 108, 109, 203, 204, 205, 206, 207, 208, 209], dtype=uint8))"
]
},
"execution_count": 3,
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -118,7 +118,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 3,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -193,7 +193,7 @@
"Panoptic: Start Evaluation\n",
"-- Got UnmatchedInstancePair, will match instances\n",
"-- Got MatchedInstancePair, will evaluate instances\n",
"-- evaluate took 2.6646389961242676 seconds to execute.\n"
"-- evaluate took 2.4123013019561768 seconds to execute.\n"
]
}
],
Expand All @@ -202,7 +202,6 @@
"evaluator = Panoptic_Evaluator(\n",
" expected_input=UnmatchedInstancePair,\n",
" instance_matcher=NaiveThresholdMatching(),\n",
" iou_threshold=0.5,\n",
")\n",
"\n",
"result, debug_data = evaluator.evaluate(sample)"
Expand All @@ -218,7 +217,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 4,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -247,7 +246,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 5,
"metadata": {},
"outputs": [
{
Expand All @@ -271,7 +270,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 6,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -326,6 +325,13 @@
"# get dict for further processing, e.g. for pandas\n",
"pprint(\"results dict: \", result.to_dict())"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -344,7 +350,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.13"
"version": "3.11.6"
}
},
"nbformat": 4,
Expand Down