Skip to content

Commit

Permalink
mics: save figure as svg
Browse files Browse the repository at this point in the history
  • Loading branch information
miltondp committed Aug 12, 2024
1 parent cd307ba commit dbc23da
Show file tree
Hide file tree
Showing 2 changed files with 8 additions and 147 deletions.
153 changes: 7 additions & 146 deletions nbs/99_manuscript/misc/01-data_with_substructures.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -60,12 +60,6 @@
"execution_count": 1,
"id": "2dcd0e52-236a-44cd-9cd9-71cca1232338",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:04.050362Z",
"iopub.status.busy": "2023-11-20T15:42:04.050025Z",
"iopub.status.idle": "2023-11-20T15:42:04.851583Z",
"shell.execute_reply": "2023-11-20T15:42:04.851239Z"
},
"papermill": {
"duration": 0.809772,
"end_time": "2023-11-20T15:42:04.853250",
Expand Down Expand Up @@ -112,12 +106,6 @@
"execution_count": 2,
"id": "3e9781c8-faf2-41ec-a5c3-ab84dec6a7fa",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:04.876161Z",
"iopub.status.busy": "2023-11-20T15:42:04.876077Z",
"iopub.status.idle": "2023-11-20T15:42:04.878289Z",
"shell.execute_reply": "2023-11-20T15:42:04.877978Z"
},
"papermill": {
"duration": 0.009172,
"end_time": "2023-11-20T15:42:04.879490",
Expand Down Expand Up @@ -154,12 +142,6 @@
"execution_count": 3,
"id": "f869a719-5302-4c5b-b496-0878617ea3d3",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:04.900870Z",
"iopub.status.busy": "2023-11-20T15:42:04.900777Z",
"iopub.status.idle": "2023-11-20T15:42:04.904748Z",
"shell.execute_reply": "2023-11-20T15:42:04.904473Z"
},
"papermill": {
"duration": 0.011527,
"end_time": "2023-11-20T15:42:04.906686",
Expand Down Expand Up @@ -208,12 +190,6 @@
"execution_count": 4,
"id": "90611494-e1b4-4c57-b7b9-cf96e7abbfd3",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:04.928844Z",
"iopub.status.busy": "2023-11-20T15:42:04.928765Z",
"iopub.status.idle": "2023-11-20T15:42:04.933308Z",
"shell.execute_reply": "2023-11-20T15:42:04.932908Z"
},
"papermill": {
"duration": 0.011492,
"end_time": "2023-11-20T15:42:04.934585",
Expand All @@ -238,12 +214,6 @@
"execution_count": 5,
"id": "e5076d0b-4614-4f67-8c0e-7965f53d6d5b",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:04.946428Z",
"iopub.status.busy": "2023-11-20T15:42:04.946271Z",
"iopub.status.idle": "2023-11-20T15:42:04.951280Z",
"shell.execute_reply": "2023-11-20T15:42:04.950760Z"
},
"papermill": {
"duration": 0.012419,
"end_time": "2023-11-20T15:42:04.952624",
Expand All @@ -264,12 +234,6 @@
"execution_count": 6,
"id": "5bcac844-f64a-4b31-82e8-1ef58d8a19e1",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:04.965338Z",
"iopub.status.busy": "2023-11-20T15:42:04.965050Z",
"iopub.status.idle": "2023-11-20T15:42:04.969707Z",
"shell.execute_reply": "2023-11-20T15:42:04.969137Z"
},
"papermill": {
"duration": 0.012945,
"end_time": "2023-11-20T15:42:04.971227",
Expand Down Expand Up @@ -300,12 +264,6 @@
"execution_count": 7,
"id": "04b1607e-3a52-4b60-a71b-e2118fc53015",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:04.983803Z",
"iopub.status.busy": "2023-11-20T15:42:04.983615Z",
"iopub.status.idle": "2023-11-20T15:42:04.993798Z",
"shell.execute_reply": "2023-11-20T15:42:04.993227Z"
},
"papermill": {
"duration": 0.018191,
"end_time": "2023-11-20T15:42:04.995323",
Expand Down Expand Up @@ -400,12 +358,6 @@
"execution_count": 8,
"id": "9ce32b94-87b1-4608-91ae-38d2b2176fbd",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.008785Z",
"iopub.status.busy": "2023-11-20T15:42:05.008297Z",
"iopub.status.idle": "2023-11-20T15:42:05.133169Z",
"shell.execute_reply": "2023-11-20T15:42:05.132734Z"
},
"papermill": {
"duration": 0.13258,
"end_time": "2023-11-20T15:42:05.133957",
Expand Down Expand Up @@ -442,12 +394,6 @@
"execution_count": 9,
"id": "a4e3f6ff-e904-4dd2-8cb0-63ce1d9ee390",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.149896Z",
"iopub.status.busy": "2023-11-20T15:42:05.149521Z",
"iopub.status.idle": "2023-11-20T15:42:05.152095Z",
"shell.execute_reply": "2023-11-20T15:42:05.151707Z"
},
"papermill": {
"duration": 0.014974,
"end_time": "2023-11-20T15:42:05.152824",
Expand Down Expand Up @@ -484,12 +430,6 @@
"execution_count": 10,
"id": "1b869c31-11c5-4d1b-81cc-3eec5df478b1",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.169177Z",
"iopub.status.busy": "2023-11-20T15:42:05.168688Z",
"iopub.status.idle": "2023-11-20T15:42:05.176073Z",
"shell.execute_reply": "2023-11-20T15:42:05.175425Z"
},
"papermill": {
"duration": 0.012977,
"end_time": "2023-11-20T15:42:05.176938",
Expand All @@ -514,12 +454,6 @@
"execution_count": 11,
"id": "3c01b5d7-f94a-448f-9b55-ac334497865f",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.185466Z",
"iopub.status.busy": "2023-11-20T15:42:05.185077Z",
"iopub.status.idle": "2023-11-20T15:42:05.189947Z",
"shell.execute_reply": "2023-11-20T15:42:05.189444Z"
},
"papermill": {
"duration": 0.010105,
"end_time": "2023-11-20T15:42:05.190811",
Expand All @@ -540,12 +474,6 @@
"execution_count": 12,
"id": "8bb5c902-7f6d-439e-863e-7588159a23ca",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.199263Z",
"iopub.status.busy": "2023-11-20T15:42:05.198946Z",
"iopub.status.idle": "2023-11-20T15:42:05.203118Z",
"shell.execute_reply": "2023-11-20T15:42:05.202524Z"
},
"papermill": {
"duration": 0.009354,
"end_time": "2023-11-20T15:42:05.203954",
Expand Down Expand Up @@ -576,12 +504,6 @@
"execution_count": 13,
"id": "677299f5-6906-4068-94fa-156cf54ee487",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.212620Z",
"iopub.status.busy": "2023-11-20T15:42:05.212197Z",
"iopub.status.idle": "2023-11-20T15:42:05.219813Z",
"shell.execute_reply": "2023-11-20T15:42:05.219367Z"
},
"papermill": {
"duration": 0.01286,
"end_time": "2023-11-20T15:42:05.220607",
Expand Down Expand Up @@ -676,12 +598,6 @@
"execution_count": 14,
"id": "e5f89c44-b7d3-4fba-b325-806887d538d7",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.229060Z",
"iopub.status.busy": "2023-11-20T15:42:05.228898Z",
"iopub.status.idle": "2023-11-20T15:42:05.382160Z",
"shell.execute_reply": "2023-11-20T15:42:05.381744Z"
},
"papermill": {
"duration": 0.159255,
"end_time": "2023-11-20T15:42:05.383709",
Expand Down Expand Up @@ -718,12 +634,6 @@
"execution_count": 15,
"id": "ed27b36e-6da9-44db-98b8-7f60b9ded22b",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.404847Z",
"iopub.status.busy": "2023-11-20T15:42:05.404752Z",
"iopub.status.idle": "2023-11-20T15:42:05.407644Z",
"shell.execute_reply": "2023-11-20T15:42:05.407270Z"
},
"papermill": {
"duration": 0.015908,
"end_time": "2023-11-20T15:42:05.408864",
Expand Down Expand Up @@ -763,12 +673,6 @@
"execution_count": 16,
"id": "d7ebe017-5ae6-4d4b-94b7-3367d96626ce",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.446435Z",
"iopub.status.busy": "2023-11-20T15:42:05.446257Z",
"iopub.status.idle": "2023-11-20T15:42:05.452245Z",
"shell.execute_reply": "2023-11-20T15:42:05.451660Z"
},
"papermill": {
"duration": 0.017549,
"end_time": "2023-11-20T15:42:05.453599",
Expand All @@ -793,12 +697,6 @@
"execution_count": 17,
"id": "3e491c19-2a36-436f-a5f8-e2dcc405304c",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.472229Z",
"iopub.status.busy": "2023-11-20T15:42:05.471864Z",
"iopub.status.idle": "2023-11-20T15:42:05.476824Z",
"shell.execute_reply": "2023-11-20T15:42:05.476269Z"
},
"papermill": {
"duration": 0.015932,
"end_time": "2023-11-20T15:42:05.478110",
Expand All @@ -819,12 +717,6 @@
"execution_count": 18,
"id": "1fbcaa46-7bc0-4a4c-8d9d-88c0fde82168",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.497508Z",
"iopub.status.busy": "2023-11-20T15:42:05.497076Z",
"iopub.status.idle": "2023-11-20T15:42:05.500916Z",
"shell.execute_reply": "2023-11-20T15:42:05.500510Z"
},
"papermill": {
"duration": 0.014885,
"end_time": "2023-11-20T15:42:05.502317",
Expand Down Expand Up @@ -855,12 +747,6 @@
"execution_count": 19,
"id": "9103bafa-218d-4bed-aaa5-603855efccce",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.518497Z",
"iopub.status.busy": "2023-11-20T15:42:05.518158Z",
"iopub.status.idle": "2023-11-20T15:42:05.525425Z",
"shell.execute_reply": "2023-11-20T15:42:05.525003Z"
},
"papermill": {
"duration": 0.014383,
"end_time": "2023-11-20T15:42:05.526198",
Expand Down Expand Up @@ -955,12 +841,6 @@
"execution_count": 20,
"id": "c6dd608a-8389-44f4-b042-10a67c6b913d",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.536329Z",
"iopub.status.busy": "2023-11-20T15:42:05.536164Z",
"iopub.status.idle": "2023-11-20T15:42:05.651584Z",
"shell.execute_reply": "2023-11-20T15:42:05.651256Z"
},
"papermill": {
"duration": 0.122491,
"end_time": "2023-11-20T15:42:05.653440",
Expand Down Expand Up @@ -997,12 +877,6 @@
"execution_count": 21,
"id": "5a996e5a-d5e4-4369-a577-c9db247cef21",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.676503Z",
"iopub.status.busy": "2023-11-20T15:42:05.676416Z",
"iopub.status.idle": "2023-11-20T15:42:05.679092Z",
"shell.execute_reply": "2023-11-20T15:42:05.678740Z"
},
"papermill": {
"duration": 0.015754,
"end_time": "2023-11-20T15:42:05.680310",
Expand Down Expand Up @@ -1059,12 +933,6 @@
"execution_count": 22,
"id": "603dae3d-0fbe-4fe0-8639-181ba6f13a20",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.739905Z",
"iopub.status.busy": "2023-11-20T15:42:05.739483Z",
"iopub.status.idle": "2023-11-20T15:42:05.746259Z",
"shell.execute_reply": "2023-11-20T15:42:05.745832Z"
},
"papermill": {
"duration": 0.015066,
"end_time": "2023-11-20T15:42:05.747143",
Expand Down Expand Up @@ -1103,12 +971,6 @@
"execution_count": 23,
"id": "0109f1d9-22ff-42fd-8bf8-ab84f449cbbd",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.789350Z",
"iopub.status.busy": "2023-11-20T15:42:05.789192Z",
"iopub.status.idle": "2023-11-20T15:42:05.797545Z",
"shell.execute_reply": "2023-11-20T15:42:05.797140Z"
},
"papermill": {
"duration": 0.015054,
"end_time": "2023-11-20T15:42:05.798329",
Expand Down Expand Up @@ -1163,12 +1025,6 @@
"execution_count": 24,
"id": "55ecad23-cf11-4ed5-a81d-c7faa16ad8b9",
"metadata": {
"execution": {
"iopub.execute_input": "2023-11-20T15:42:05.809867Z",
"iopub.status.busy": "2023-11-20T15:42:05.809487Z",
"iopub.status.idle": "2023-11-20T15:42:09.164387Z",
"shell.execute_reply": "2023-11-20T15:42:09.164057Z"
},
"papermill": {
"duration": 3.363718,
"end_time": "2023-11-20T15:42:09.167366",
Expand Down Expand Up @@ -1242,7 +1098,7 @@
" )\n",
"\n",
" plt.savefig(\n",
" OUTPUT_FIGURE_DIR / \"clusters.png\",\n",
" OUTPUT_FIGURE_DIR / \"clusters.svg\",\n",
" # rasterized=True,\n",
" dpi=300,\n",
" bbox_inches=\"tight\",\n",
Expand Down Expand Up @@ -1271,7 +1127,12 @@
"metadata": {
"jupytext": {
"cell_metadata_filter": "all,-execution,-papermill,-trusted",
"notebook_metadata_filter": "-jupytext.text_representation.jupytext_version"
"notebook_metadata_filter": "-jupytext.text_representation.jupytext_version",
"text_representation": {
"extension": ".py",
"format_name": "percent",
"format_version": "1.3"
}
},
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
Expand Down
2 changes: 1 addition & 1 deletion nbs/99_manuscript/misc/py/01-data_with_substructures.py
Original file line number Diff line number Diff line change
Expand Up @@ -256,7 +256,7 @@ def get_cm_line_points(x, y, max_parts, parts):
)

plt.savefig(
OUTPUT_FIGURE_DIR / "clusters.png",
OUTPUT_FIGURE_DIR / "clusters.svg",
# rasterized=True,
dpi=300,
bbox_inches="tight",
Expand Down

0 comments on commit dbc23da

Please sign in to comment.