Skip to content

Commit cdc9339

Browse files
ascibiszascibisz
authored
Merge pull request #154 from simularium/fix/update-examples
Fix/update examples
2 parents 51800c6 + b064aa0 commit cdc9339

14 files changed

+81
-43
lines changed

‎Justfile‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -32,6 +32,7 @@ lint:
3232
# run tests
3333
test:
3434
pytest --cov-report xml --cov-report html --cov=simulariumio simulariumio/tests
35+
pytest --nbmake "./examples"
3536

3637
# run lint and then run tests
3738
build:

‎examples/Tutorial_custom.ipynb‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -208,11 +208,12 @@
208208
" radii=np.ones(shape=(total_steps, n_agents)),\n",
209209
" n_subpoints=points_per_fiber * np.ones(shape=(total_steps, n_agents)),\n",
210210
" subpoints=box_size * np.random.uniform(\n",
211-
" size=(total_steps, n_agents, points_per_fiber, 3)) - box_size * 0.5,\n",
211+
" size=(total_steps, n_agents, points_per_fiber * 3)) - box_size * 0.5,\n",
212212
" display_data={\n",
213213
" type_names[0][0]: DisplayData(\n",
214214
" name=\"X\",\n",
215215
" color=\"#0080ff\",\n",
216+
" display_type=DISPLAY_TYPE.SPHERE,\n",
216217
" ),\n",
217218
" },\n",
218219
" ),\n",

‎examples/Tutorial_cytosim.ipynb‎

Lines changed: 9 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -96,11 +96,13 @@
9696
" display_data={\n",
9797
" 1 : DisplayData(\n",
9898
" name=\"microtubule\",\n",
99-
" radius=0.01\n",
99+
" radius=0.01,\n",
100+
" display_type=DISPLAY_TYPE.FIBER\n",
100101
" ),\n",
101102
" 2 : DisplayData(\n",
102103
" name=\"actin\",\n",
103-
" radius=0.01\n",
104+
" radius=0.01,\n",
105+
" display_type=DISPLAY_TYPE.FIBER\n",
104106
" )\n",
105107
" }\n",
106108
" ),\n",
@@ -111,11 +113,13 @@
111113
" display_data={\n",
112114
" 1 : DisplayData(\n",
113115
" name=\"aster\",\n",
114-
" radius=0.1\n",
116+
" radius=0.1,\n",
117+
" display_type=DISPLAY_TYPE.SPHERE\n",
115118
" ),\n",
116119
" 2 : DisplayData(\n",
117120
" name=\"vesicle\",\n",
118-
" radius=0.02\n",
121+
" radius=0.02,\n",
122+
" display_type=DISPLAY_TYPE.SPHERE\n",
119123
" )\n",
120124
" }\n",
121125
" ),\n",
@@ -149,6 +153,7 @@
149153
" name=\"motor complex\",\n",
150154
" radius=0.01,\n",
151155
" color=\"#bf95d4\",\n",
156+
" display_type=DISPLAY_TYPE.SPHERE\n",
152157
" )\n",
153158
" },\n",
154159
" position_indices=[3, 4, 5]\n",

‎examples/Tutorial_filters.ipynb‎

Lines changed: 33 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,7 @@
1515
"source": [
1616
"from IPython.display import Image\n",
1717
"import numpy as np\n",
18-
"from simulariumio import FileConverter, TrajectoryData, AgentData, BinaryWriter, InputFileData\n",
18+
"from simulariumio import FileConverter, TrajectoryData, AgentData, BinaryWriter, InputFileData, DisplayData, DISPLAY_TYPE\n",
1919
"from simulariumio.filters import EveryNthAgentFilter"
2020
]
2121
},
@@ -59,7 +59,7 @@
5959
"text": [
6060
"Reading Simularium JSON -------------\n",
6161
"Updated TrajectoryInfo v1 -> v3\n",
62-
"original dim = 3 timesteps X 17 agents X 6 subpoints\n"
62+
"original dim = 3 timesteps X 17 agents X 18 subpoints\n"
6363
]
6464
}
6565
],
@@ -72,6 +72,36 @@
7272
" \"aster_pull3D_couples_actin_solid_3_frames.json\"\n",
7373
" ),\n",
7474
" ),\n",
75+
" display_data={\n",
76+
" 1: DisplayData(\n",
77+
" name=\"microtubule\",\n",
78+
" display_type=DISPLAY_TYPE.FIBER,\n",
79+
" ),\n",
80+
" 2: DisplayData(\n",
81+
" name=\"actin\",\n",
82+
" display_type=DISPLAY_TYPE.FIBER,\n",
83+
" ),\n",
84+
" 3: DisplayData(\n",
85+
" name=\"aster\",\n",
86+
" display_type=DISPLAY_TYPE.SPHERE,\n",
87+
" ),\n",
88+
" 4: DisplayData(\n",
89+
" name=\"vesicle\",\n",
90+
" display_type=DISPLAY_TYPE.SPHERE,\n",
91+
" ),\n",
92+
" 5: DisplayData(\n",
93+
" name=\"kinesin\",\n",
94+
" display_type=DISPLAY_TYPE.SPHERE,\n",
95+
" ),\n",
96+
" 6: DisplayData(\n",
97+
" name=\"dynein\",\n",
98+
" display_type=DISPLAY_TYPE.SPHERE,\n",
99+
" ),\n",
100+
" 7: DisplayData(\n",
101+
" name=\"motor complex\",\n",
102+
" display_type=DISPLAY_TYPE.SPHERE,\n",
103+
" ),\n",
104+
" },\n",
75105
")"
76106
]
77107
},
@@ -112,7 +142,7 @@
112142
" default_n=2,\n",
113143
" ),\n",
114144
"])\n",
115-
"BinaryWriter.save(filtered_data, \"example_filter_reduce\")"
145+
"BinaryWriter.save(filtered_data, \"example_filter_reduce\", False)"
116146
]
117147
},
118148
{

‎examples/Tutorial_mcell.ipynb‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -95,9 +95,11 @@
9595
" ),\n",
9696
" \"b\" : DisplayData(\n",
9797
" name=\"Molecule B\",\n",
98+
" display_type=DISPLAY_TYPE.SPHERE,\n",
9899
" ),\n",
99100
" \"t2\" : DisplayData(\n",
100101
" name=\"Receptor T2\",\n",
102+
" display_type=DISPLAY_TYPE.SPHERE,\n",
101103
" color=\"#ff1493\",\n",
102104
" ),\n",
103105
" },\n",

‎examples/Tutorial_md.ipynb‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -97,6 +97,7 @@
9797
" # but you can override them by providing colors and/or names here\n",
9898
" \"S\": DisplayData(\n",
9999
" name=\"Sulfur\",\n",
100+
" display_type=DISPLAY_TYPE.SPHERE,\n",
100101
" color=\"#FF00FF\",\n",
101102
" ),\n",
102103
" },\n",

‎examples/Tutorial_medyan.ipynb‎

Lines changed: 10 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@
1616
"from IPython.display import Image\n",
1717
"import numpy as np\n",
1818
"from simulariumio.medyan import MedyanConverter, MedyanData\n",
19-
"from simulariumio import MetaData, DisplayData, ModelMetaData, BinaryWriter, InputFileData\n",
19+
"from simulariumio import MetaData, DisplayData, ModelMetaData, BinaryWriter, InputFileData, DISPLAY_TYPE\n",
2020
"from simulariumio.filters import TranslateFilter"
2121
]
2222
},
@@ -87,33 +87,39 @@
8787
" filament_display_data={\n",
8888
" 0: DisplayData(\n",
8989
" name=\"Filament\",\n",
90+
" display_type=DISPLAY_TYPE.SPHERE,\n",
9091
" radius=5.0,\n",
9192
" color=\"#ff1493\",\n",
9293
" ),\n",
9394
" },\n",
9495
" linker_display_data={\n",
9596
" 0: DisplayData(\n",
9697
" name=\"LinkerA\",\n",
98+
" display_type=DISPLAY_TYPE.SPHERE,\n",
9799
" radius=8.0,\n",
98100
" color=\"#ffffff\",\n",
99101
" ),\n",
100102
" 1: DisplayData(\n",
101103
" name=\"LinkerB\",\n",
104+
" display_type=DISPLAY_TYPE.SPHERE,\n",
102105
" radius=8.0,\n",
103106
" ),\n",
104107
" 2: DisplayData(\n",
105108
" name=\"LinkerC\",\n",
109+
" display_type=DISPLAY_TYPE.SPHERE,\n",
106110
" radius=8.0,\n",
107111
" ),\n",
108112
" },\n",
109113
" motor_display_data={\n",
110114
" 1: DisplayData(\n",
111115
" name=\"Motor\",\n",
116+
" display_type=DISPLAY_TYPE.SPHERE,\n",
112117
" radius=2.0,\n",
113118
" color=\"#0080ff\",\n",
114119
" ),\n",
115120
" },\n",
116-
" agents_with_endpoints=[\"Motor\"]\n",
121+
" agents_with_endpoints=[\"Motor\"],\n",
122+
" center=True,\n",
117123
")"
118124
]
119125
},
@@ -128,9 +134,7 @@
128134
"cell_type": "markdown",
129135
"metadata": {},
130136
"source": [
131-
"Once your data is shaped like in the `example_data` object, you can use the converter to generate the file at the given path:\n",
132-
"\n",
133-
"(since MEDYAN coordinates are all positive, use a `TranslateFilter` to center the data in the viewer.)"
137+
"Once your data is shaped like in the `example_data` object, you can use the converter to generate the file at the given path:"
134138
]
135139
},
136140
{
@@ -151,15 +155,7 @@
151155
}
152156
],
153157
"source": [
154-
"c = MedyanConverter(example_data)\n",
155-
"translation_magnitude = -(box_size * scale) / 2\n",
156-
"filtered_data = c.filter_data([\n",
157-
" TranslateFilter(\n",
158-
" translation_per_type={},\n",
159-
" default_translation=translation_magnitude * np.ones(3)\n",
160-
" ),\n",
161-
"])\n",
162-
"BinaryWriter.save(filtered_data, \"example_medyan\")"
158+
"MedyanConverter(example_data).save(\"example_medyan\")"
163159
]
164160
},
165161
{

‎examples/Tutorial_physicell.ipynb‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -70,7 +70,7 @@
7070
"\n",
7171
"example_data = PhysicellData(\n",
7272
" timestep=360.0,\n",
73-
" path_to_output_dir=\"../simulariumio/tests/data/physicell/output/\",\n",
73+
" path_to_output_dir=\"../simulariumio/tests/data/physicell/default_output/\",\n",
7474
" meta_data=MetaData(\n",
7575
" box_size=np.array([box_size, box_size, 100.0]),\n",
7676
" scale_factor=0.01,\n",
@@ -99,6 +99,7 @@
9999
" ),\n",
100100
" 1: DisplayData(\n",
101101
" name=\"motile tumor cell\",\n",
102+
" display_type=DISPLAY_TYPE.SPHERE,\n",
102103
" color=\"#0080ff\",\n",
103104
" ),\n",
104105
" },\n",

‎examples/Tutorial_readdy.ipynb‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -91,6 +91,7 @@
9191
" \"B\": DisplayData(\n",
9292
" name=\"B\",\n",
9393
" radius=2.0,\n",
94+
" display_type=DISPLAY_TYPE.SPHERE,\n",
9495
" color=\"#0080ff\",\n",
9596
" ),\n",
9697
" },\n",

‎examples/Tutorial_smoldyn.ipynb‎

Lines changed: 4 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -101,11 +101,13 @@
101101
" \"green(solution)\": DisplayData(\n",
102102
" name=\"A\",\n",
103103
" radius=2.0,\n",
104+
" display_type=DISPLAY_TYPE.SPHERE,\n",
104105
" color=\"#0080ff\",\n",
105106
" ),\n",
106107
" },\n",
107108
" time_units=UnitData(\"ns\"), # nanoseconds\n",
108109
" spatial_units=UnitData(\"nm\"), # nanometers\n",
110+
" center=True,\n",
109111
")"
110112
]
111113
},
@@ -120,9 +122,7 @@
120122
"cell_type": "markdown",
121123
"metadata": {},
122124
"source": [
123-
"Once your data is shaped like in the `example_data` object, you can use the converter to generate the file at the given path:\n",
124-
"\n",
125-
"(since this model's coordinates are all positive, use a `TranslateFilter` to center the data in the viewer.)"
125+
"Once your data is shaped like in the `example_data` object, you can use the converter to generate the file at the given path:"
126126
]
127127
},
128128
{
@@ -143,15 +143,7 @@
143143
}
144144
],
145145
"source": [
146-
"c = SmoldynConverter(example_data)\n",
147-
"translation_magnitude = -box_size / 2\n",
148-
"filtered_data = c.filter_data([\n",
149-
" TranslateFilter(\n",
150-
" translation_per_type={},\n",
151-
" default_translation=translation_magnitude * np.ones(3)\n",
152-
" ),\n",
153-
"])\n",
154-
"BinaryWriter.save(filtered_data, \"example_smoldyn\")"
146+
"SmoldynConverter(example_data).save(\"example_smoldyn\")"
155147
]
156148
},
157149
{

0 commit comments

Comments
 (0)