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Mem3DG converter (#195)
* mem3dg converter * add link to source of input file data * default scale_factor to 1.0 * add unit tests * lint fixes * update justfile to install mem3dg dependencies * .obj file url should just be the file name, since it will be uploaded alongside the simularium file * fix typo
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‎Justfile‎

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@@ -23,7 +23,7 @@ clean:
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# install with all deps (and setup conda env with readdy)
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install:
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conda env update --file environment.yml
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pip install -e .[lint,test,docs,dev,mcell,physicell,md,cellpack]
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pip install -e .[lint,test,docs,dev,mcell,physicell,md,cellpack,mem3dg]
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# lint, format, and check all files
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lint:

‎examples/Tutorial_mem3dg.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Simularium Conversion Tutorial : Mem3DG .nc Data"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from IPython.display import Image\n",
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"\n",
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"import numpy as np\n",
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"\n",
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"from simulariumio.mem3dg import Mem3dgConverter, Mem3dgData\n",
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"from simulariumio import MetaData, CameraData, UnitData"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"This notebook provides example python code for converting your own simulation trajectories into the format consumed by the Simularium Viewer. It creates a .simularium file which you can drag and drop onto the viewer like this:"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"![title](img/drag_drop.gif)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# _Note:_\n",
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"To install simulariumio with all depencies needed for Mem3DG conversion, use `pip install simulariumio[mem3dg]`"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"***\n",
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"## Prepare your spatial data"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"The Simularium `Mem3dgConverter` consumes spatiotemporal data from Mem3DG .nc output files using the netCDF4 Python package. \n",
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"\n",
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"The converter requires a `Mem3dgData` object as a parameter.\n",
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"\n",
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"Unlike other simulariumio converters, the `Mem3dgConverter` will generate several `.obj` files (one per frame) in addition to the `.simularium` file. Use `output_obj_file_path` to specify where the generated obj files should be saved.\n",
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"\n",
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"The test input .nc data for this example was created using [Mem3DG's Jupyter Notebook tutorials](https://github.com/RangamaniLabUCSD/Mem3DG/blob/main/tests/python/tutorial/tutorial1.ipynb)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"box_size = 5.\n",
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"scale_factor = 10\n",
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"\n",
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"example_data = Mem3dgData(\n",
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" input_file_path=\"../simulariumio/tests/data/mem3dg/traj.nc\",\n",
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" output_obj_file_path=\".\",\n",
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" meta_data=MetaData(\n",
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" box_size=np.array([box_size, box_size, box_size]),\n",
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" trajectory_title=\"Some parameter set\",\n",
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" camera_defaults=CameraData(position=np.array([0, 0, 200])),\n",
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" scale_factor=scale_factor\n",
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" ),\n",
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" agent_color=\"#a38fba\",\n",
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" agent_name=\"my-object\",\n",
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" time_units=UnitData(\"us\", 0.2),\n",
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")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Convert and save as .simularium file"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Once your data is shaped like in the `example_data` object, you can use the converter to generate the file at the given path"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Reading Mem3DG Data -------------\n",
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"Converting Trajectory Data to JSON -------------\n",
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"Writing JSON -------------\n",
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"saved to example_mem3dg.simularium\n"
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]
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}
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],
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"source": [
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"converter = Mem3dgConverter(example_data).save(\"example_mem3dg\", binary=False)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Visualize in the Simularium viewer"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"In a supported web-browser (Firefox or Chrome), navigate to https://simularium.allencell.org/ and import your file into the view.\n",
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"\n",
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"**Note:** In order to view your data in simularium, you must import the generated .simularium file _and_ all of the generated .obj files!"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.16"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

‎pyproject.toml‎

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@@ -57,6 +57,9 @@ cellpack = [
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nerdss = [
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"MDAnalysis>=2.0.0",
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]
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mem3dg = [
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"netCDF4",
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]
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tutorial = [
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"jupyter",
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"scipy>=1.5.2",

‎simulariumio/mem3dg/__init__.py‎

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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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from .mem3dg_converter import Mem3dgConverter # noqa: F401
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from .mem3dg_data import Mem3dgData # noqa: F401

‎simulariumio/mem3dg/mem3dg_converter.py‎

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from netCDF4 import Dataset
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import numpy as np
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from pathlib import Path
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from ..trajectory_converter import TrajectoryConverter
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from ..data_objects import (
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AgentData,
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TrajectoryData,
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DimensionData,
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DisplayData,
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)
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from ..constants import DISPLAY_TYPE
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from ..exceptions import InputDataError
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from .mem3dg_data import Mem3dgData
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class Mem3dgConverter(TrajectoryConverter):
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def __init__(
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self,
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input_data: Mem3dgData,
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):
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"""
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Parameters
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----------
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input_data : Mem3dgData
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An object containing info for reading
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Mem3DG simulation trajectory output
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"""
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self._data = self._read(input_data)
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def write_to_obj(self, filepath, data, frame):
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# Extract XYZ coordinates for vertices
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coordinates = np.array(
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data.groups["Trajectory"].variables["coordinates"][frame]
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)
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coordinates = np.reshape(coordinates, (-1, 3))
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# Extract indices of vertices to make faces (all triangles)
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topology = np.array(data.groups["Trajectory"].variables["topology"][frame])
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topology = np.reshape(topology, (-1, 3))
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# change indices to be 1 indexed instead of 0 indexed for .obj files
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topology += 1
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# Generate one .obj file per frame
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with open(filepath, "w") as file:
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file.write(f"# Frame {frame}\n")
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for v in coordinates:
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file.write(f"v {v[0]} {v[1]} {v[2]}\n")
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for t in topology:
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file.write(f"f {t[0]} {t[1]} {t[2]}\n")
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def _read_traj_data(self, input_data: Mem3dgData) -> AgentData:
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try:
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data = Dataset(input_data.input_file_path, "r")
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n_frames = np.size(data.groups["Trajectory"].variables["time"])
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except Exception as e:
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raise InputDataError(f"Error reading input Mem3DG data: {e}")
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# for now, we are representing converted Mem3DG trajectories as one
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# unique mesh agent per frame
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dimensions = DimensionData(total_steps=n_frames, max_agents=1)
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agent_data = AgentData.from_dimensions(dimensions)
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agent_data.n_timesteps = n_frames
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base_agent_name = input_data.agent_name or "object"
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for frame in range(n_frames):
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agent_data.times[frame] = data.groups["Trajectory"].variables["time"][frame]
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agent_data.n_agents[frame] = 1
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output_file_path = Path(input_data.output_obj_file_path) / f"{frame}.obj"
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self.write_to_obj(output_file_path, data, frame)
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agent_data.radii[frame][0] = input_data.meta_data.scale_factor
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agent_data.unique_ids[frame][0] = frame
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name = str(frame)
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agent_data.types[frame].append(name)
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object_display_data = DisplayData(
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name=f"{base_agent_name}#frame{frame}",
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display_type=DISPLAY_TYPE.OBJ,
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url=f"{frame}.obj",
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color=input_data.agent_color,
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)
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agent_data.display_data[name] = object_display_data
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return agent_data
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def _read(self, input_data: Mem3dgData) -> TrajectoryData:
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"""
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Return a TrajectoryData object containing the Mem3DG data
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"""
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print("Reading Mem3DG Data -------------")
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if input_data.meta_data.scale_factor is None:
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input_data.meta_data.scale_factor = 1.0
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agent_data = self._read_traj_data(input_data)
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input_data.spatial_units.multiply(1.0 / input_data.meta_data.scale_factor)
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input_data.meta_data._set_box_size()
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result = TrajectoryData(
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meta_data=input_data.meta_data,
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agent_data=agent_data,
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time_units=input_data.time_units,
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spatial_units=input_data.spatial_units,
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plots=input_data.plots,
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)
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return result

‎simulariumio/mem3dg/mem3dg_data.py‎

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from ..data_objects import MetaData, UnitData
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from typing import List, Dict, Any
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class Mem3dgData:
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input_file_path: str
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output_obj_file_path: str
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meta_data: MetaData
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agent_name: str
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agent_color: str
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time_units: UnitData
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spatial_units: UnitData
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plots: List[Dict[str, Any]]
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def __init__(
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self,
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input_file_path: str,
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output_obj_file_path: str = None,
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meta_data: MetaData = None,
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agent_name: str = None,
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agent_color: str = None,
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time_units: UnitData = None,
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spatial_units: UnitData = None,
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plots: List[Dict[str, Any]] = None,
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):
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"""
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Parameters
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----------
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input_file_path : str
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The path to the .nc file output by Mem3DG for this trajectory.
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output_obj_file_path : str (optional)
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The path to the directory where output .obj files will be saved
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to. If nothing is provided, the output .obj files will be saved
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to the current directory.
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meta_data : MetaData
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An object containing metadata for the trajectory
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including box size, scale factor, and camera defaults
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agent_name: str (optional)
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This converter generates it's own DisplayData, but the agent name
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can optionally be overridden here. This will change the agent
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name that is displayed on the side column in simularium
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agent_color: string (optional)
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This converter generates it's own DisplayData, but the agent color
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can optionally be overridden here with a hex value for the color to
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display, e.g "#FFFFFF"
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Default: Use default colors from Simularium Viewer
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time_units: UnitData (optional)
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multiplier and unit name for time values
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Default: 1.0 second
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spatial_units: UnitData (optional)
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multiplier and unit name for spatial values
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(including positions, radii, and box size)
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Default: 1.0 meter
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plots : List[Dict[str, Any]] (optional)
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An object containing plot data already
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in Simularium format
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"""
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self.input_file_path = input_file_path
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self.output_obj_file_path = output_obj_file_path or "."
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self.meta_data = meta_data or MetaData()
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self.agent_name = agent_name
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self.agent_color = agent_color
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self.time_units = time_units or UnitData("s")
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self.spatial_units = spatial_units or UnitData("m")
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self.plots = plots or []

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