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Merge pull request #119 from simularium/fix/update-trajectory-tests
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Rewrite Trajectory Converter Tests
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@ascibisz
ascibisz committed Dec 2, 2022
1 parent e98680a commit 203ef4a
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Showing 16 changed files with 4,857 additions and 6,638 deletions.
7 changes: 5 additions & 2 deletions simulariumio/md/md_converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@

from ..trajectory_converter import TrajectoryConverter
from ..data_objects import TrajectoryData, AgentData, DimensionData, DisplayData
from ..constants import JMOL_COLORS
from ..constants import DISPLAY_TYPE, JMOL_COLORS
from .md_data import MdData

###############################################################################
Expand Down Expand Up @@ -115,7 +115,10 @@ def _get_display_data_for_type(
display_data = copy.copy(input_data.display_data[element_type])
display_data.name = type_name
else:
display_data = DisplayData(name=type_name)
display_data = DisplayData(
name=type_name,
display_type=DISPLAY_TYPE.SPHERE
)
if display_data.color:
return display_data
display_data.color = color
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1 change: 1 addition & 0 deletions simulariumio/readdy/readdy_converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,6 +89,7 @@ def _get_agent_data(
agent_index
]
result.types[time_index].append(display_data.name)
result.display_data[display_data.name] = display_data
result.positions[time_index][new_agent_index] = (
input_data.meta_data.scale_factor
* positions[time_index][agent_index]
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230 changes: 229 additions & 1 deletion simulariumio/tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,53 @@ def default_agents_type_mapping() -> Dict[str, Any]:
}


def minimal_custom_type_mappings() -> Dict[str, Any]:
return {
"0": {
"name": "C",
"geometry": {
"displayType": "SPHERE",
},
},
"1": {
"name": "U",
"geometry": {
"displayType": "SPHERE",
},
},
"2": {
"name": "L",
"geometry": {
"displayType": "SPHERE",
},
},
"3": {
"name": "S",
"geometry": {
"displayType": "SPHERE",
},
},
"4": {
"name": "O",
"geometry": {
"displayType": "SPHERE",
},
},
"5": {
"name": "Y",
"geometry": {
"displayType": "SPHERE",
},
},
"6": {
"name": "W",
"geometry": {
"displayType": "SPHERE",
},
},
}


def three_default_agents() -> TrajectoryData:
return TrajectoryData(
meta_data=MetaData(
Expand Down Expand Up @@ -173,6 +220,75 @@ def three_default_agents() -> TrajectoryData:
)


def minimal_custom_data() -> TrajectoryData:
return TrajectoryData(
meta_data=MetaData(),
agent_data=AgentData(
times=0.5 * np.array(list(range(3))),
n_agents=np.array(3 * [3]),
viz_types=np.array(3 * [3 * [1000.0]]),
unique_ids=np.array([[0.0, 1.0, 2.0], [0.0, 1.0, 2.0], [0.0, 1.0, 2.0]]),
types=[["C", "U", "C"], ["U", "L", "S"], ["O", "Y", "W"]],
display_data={
"C": DisplayData(
name="C",
display_type=DISPLAY_TYPE.SPHERE,
),
"W": DisplayData(
name="W",
display_type=DISPLAY_TYPE.SPHERE,
),
"S": DisplayData(
name="S",
display_type=DISPLAY_TYPE.SPHERE,
),
"Y": DisplayData(
name="Y",
display_type=DISPLAY_TYPE.SPHERE,
),
"L": DisplayData(
name="L",
display_type=DISPLAY_TYPE.SPHERE,
),
"U": DisplayData(
name="U",
display_type=DISPLAY_TYPE.SPHERE,
),
"O": DisplayData(
name="O",
display_type=DISPLAY_TYPE.SPHERE,
),
},
positions=np.array(
[
[
[4.89610492, -29.81564851, 40.77254057],
[43.43048197, 48.00424379, -36.02881338],
[29.84924588, -38.02769707, 2.46644825],
],
[
[-43.37181102, -13.41127423, -17.31316927],
[9.62132397, 13.4774314, -20.30846039],
[41.41039848, -45.85543786, 49.06208485],
],
[
[-24.91450698, -44.79360525, 13.32273796],
[4.10861266, 43.86451151, 21.93697483],
[-7.16740679, -13.06491594, 44.97026158],
],
]
),
radii=np.array(
[
[8.38656327, 6.18568039, 6.61459206],
[5.26366739, 6.69209780, 9.88033853],
[8.91022619, 9.01379396, 8.39880154],
]
),
),
)


def test_scatter_plot() -> ScatterPlotData:
return ScatterPlotData(
title="Test Scatterplot 1",
Expand Down Expand Up @@ -286,6 +402,47 @@ def full_default_buffer() -> AgentData:
)


def fiber_agents_type_mapping() -> Dict[str, Any]:
return {
"0": {
"name": "H",
"geometry": {
"displayType": "FIBER",
},
},
"1": {
"name": "A",
"geometry": {
"displayType": "FIBER",
},
},
"2": {
"name": "C",
"geometry": {
"displayType": "FIBER",
},
},
"3": {
"name": "L",
"geometry": {
"displayType": "FIBER",
},
},
"4": {
"name": "D",
"geometry": {
"displayType": "FIBER",
},
},
"5": {
"name": "K",
"geometry": {
"displayType": "FIBER",
},
},
}


def fiber_agents() -> TrajectoryData:
return TrajectoryData(
meta_data=MetaData(
Expand Down Expand Up @@ -474,6 +631,77 @@ def fiber_agents() -> TrajectoryData:
)


def mixed_agents_type_mapping() -> Dict[str, Any]:
return {
"0": {
"name": "H",
"geometry": {
"displayType": "SPHERE",
},
},
"1": {
"name": "A",
"geometry": {
"displayType": "FIBER",
},
},
"2": {
"name": "C",
"geometry": {
"displayType": "FIBER",
},
},
"3": {
"name": "X",
"geometry": {
"displayType": "SPHERE",
},
},
"4": {
"name": "J",
"geometry": {
"displayType": "FIBER",
},
},
"5": {
"name": "L",
"geometry": {
"displayType": "FIBER",
},
},
"6": {
"name": "D",
"geometry": {
"displayType": "SPHERE",
},
},
"7": {
"name": "U",
"geometry": {
"displayType": "FIBER",
},
},
"8": {
"name": "E",
"geometry": {
"displayType": "SPHERE",
},
},
"9": {
"name": "Q",
"geometry": {
"displayType": "SPHERE",
},
},
"10": {
"name": "K",
"geometry": {
"displayType": "FIBER",
},
},
}


def mixed_agents() -> TrajectoryData:
return TrajectoryData(
meta_data=MetaData(
Expand Down Expand Up @@ -818,7 +1046,7 @@ def mixed_agents() -> TrajectoryData:
),
},
),
time_units=UnitData("s"),
time_units=UnitData("s", 2.0),
spatial_units=UnitData("um"),
plots=["plot data goes here"],
)
Expand Down
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