diff --git a/.gitignore b/.gitignore
index c93c2451ee6958af633a4e24fd66c34304682f73..043b66a95a35968ee555bd349ade5dddc7a2dc0c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,6 +9,7 @@ dist
report.xml
htmlcov
docs
+env
!tests/resources/*.hdf5
*.ipynb_checkpoints
diff --git a/README.md b/README.md
index 677e3a4d077fc09e1c21b3eb3b01166e52e41268..5da734e05530add0c7ef723c9990f3634dbcd57f 100644
--- a/README.md
+++ b/README.md
@@ -32,33 +32,36 @@ import robofish.io
import numpy as np
-# By using the context, the file will be automatically validated
-with robofish.io.File("Example.hdf5", "w", world_size_cm=[100, 100], frequency_hz=25.0) as f:
- f.attrs["experiment_setup"] = "This is a simple example with made up data."
-
- # Create a single robot with 30 timesteps
- # positions are passed separately
- # orientations are passed as with two columns -> orientation_x and orientation_y
- f.create_entity(
- category="robot",
- name="robot",
- positions=np.zeros((100, 2)),
- orientations=np.ones((100, 2)) * [0, 1],
- )
-
- # Create fishes with 30 poses (x, y, orientation_rad)
- poses = np.zeros((100, 3))
- poses[:, 0] = np.arange(-50, 50)
- poses[:, 1] = np.arange(-50, 50)
- poses[:, 2] = np.arange(0, 2 * np.pi, step=2 * np.pi / 100)
- fish = f.create_entity("fish", poses=poses)
- fish.attrs["species"] = "My rotating spaghetti fish"
- fish.attrs["fish_standard_length_cm"] = 10
-
- # Show and save the file
- print(f)
- print("Poses Shape: ", f.entity_poses.shape)
-
+# Create a new robofish io file
+f = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25.0)
+f.attrs["experiment_setup"] = "This is a simple example with made up data."
+
+# Create a new robot entity. Positions and orientations are passed
+# separately in this example. Since the orientations have two columns,
+# unit vectors are assumed (orientation_x, orientation_y)
+f.create_entity(
+ category="robot",
+ name="robot",
+ positions=np.zeros((100, 2)),
+ orientations=np.ones((100, 2)) * [0, 1],
+)
+
+# Create a new fish entity.
+# In this case, we pass positions and orientations together (x, y, rad).
+# Since it is a 3 column array, orientations in radiants are assumed.
+poses = np.zeros((100, 3))
+poses[:, 0] = np.arange(-50, 50)
+poses[:, 1] = np.arange(-50, 50)
+poses[:, 2] = np.arange(0, 2 * np.pi, step=2 * np.pi / 100)
+fish = f.create_entity("fish", poses=poses)
+fish.attrs["species"] = "My rotating spaghetti fish"
+fish.attrs["fish_standard_length_cm"] = 10
+
+# Show and save the file
+print(f)
+print("Poses Shape: ", f.entity_poses.shape)
+
+f.save_as(path)
```
### Evaluation
@@ -68,7 +71,7 @@ Current modes are:
- turn
- tank_positions
- trajectories
-- follow_ii
+- follow_iid
## LICENSE
diff --git a/ci/test.py b/ci/test.py
index c6d90a39d599fc668a6a1ed525c2a940ddeeec4f..ab41980d6b6bae18e8bf990f162b20b57edd82af 100755
--- a/ci/test.py
+++ b/ci/test.py
@@ -34,7 +34,7 @@ if __name__ == "__main__":
"--prompt",
"ci",
".venv",
- ],
+ ]
)
check_call(
@@ -44,9 +44,7 @@ if __name__ == "__main__":
"pip",
"install",
str(sorted(Path("dist").glob("*.whl"))[-1].resolve()),
- ],
+ ]
)
- check_call(
- [python_venv_executable(), "-m", "pytest", "--junitxml=report.xml"],
- )
+ check_call([python_venv_executable(), "-m", "pytest", "--junitxml=report.xml"])
diff --git a/examples/example_basic.ipynb b/examples/example_basic.ipynb
index 3569083dc85945861dea2aecdba701dbfe2d3327..eba81c56c7c497751bffce4c944b4ae3212dac15 100644
--- a/examples/example_basic.ipynb
+++ b/examples/example_basic.ipynb
@@ -2,7 +2,65 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": 20,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import robofish.io\n",
+ "import numpy as np\n",
+ "\n",
+ "\n",
+ "def create_example_file(path):\n",
+ " # Create a new io file object with a 100x100cm world\n",
+ " f = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25.0)\n",
+ "\n",
+ " # create a simple obstacle, fixed in place, fixed outline\n",
+ " obstacle_outline = [[[-10, -10], [-10, 0], [0, 0], [0, -10]]]\n",
+ " obstacle_name = f.create_entity(\n",
+ " \"obstacle\", positions=[[50, 50]], orientations=[[0]], outlines=obstacle_outline\n",
+ " )\n",
+ "\n",
+ " # create a robofish with 1000 timesteps. If we would not give a name, the name would be generated to be robot_1.\n",
+ " robofish_timesteps = 1000\n",
+ " robofish_poses = np.tile([50, 50, 1, 0], (robofish_timesteps, 1))\n",
+ " robot = f.create_entity(\"robot\", name=\"robot\", poses=robofish_poses)\n",
+ "\n",
+ " # create multiple fishes with timestamps. Since we don't specify names, but only the type \"fish\" the fishes will be named [\"fish_1\", \"fish_2\", \"fish_3\"]\n",
+ " agents = 3\n",
+ " timesteps = 1000\n",
+ " # timestamps = np.linspace(0, timesteps + 1, timesteps)\n",
+ " agent_poses = np.random.random((agents, timesteps, 3))\n",
+ "\n",
+ " fishes = f.create_multiple_entities(\"fish\", agent_poses)\n",
+ "\n",
+ " # This would throw an exception if the file was invalid\n",
+ " f.validate()\n",
+ "\n",
+ " # Save file validates aswell\n",
+ " f.save_as(path)\n",
+ "\n",
+ " # Closing and opening files (just for demonstration). When opening with r+, we can read and write afterwards.\n",
+ " f.close()\n",
+ " f = robofish.io.File(path, \"r+\")\n",
+ "\n",
+ " print(\"\\nEntity Names\")\n",
+ " print(f.entity_names)\n",
+ "\n",
+ " # Get an array with all poses. As the length of poses varies per agent, it is filled up with nans.\n",
+ " print(\"\\nAll poses\")\n",
+ " print(f.entity_poses)\n",
+ "\n",
+ " # Select all entities with the category fish\n",
+ " print(\"\\nFish poses\")\n",
+ " print(f.select_entity_poses(lambda e: e.category == \"fish\"))\n",
+ "\n",
+ " print(\"\\nFinal file\")\n",
+ " print(f)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 21,
"metadata": {},
"outputs": [
{
@@ -14,29 +72,29 @@
"['fish_1', 'fish_2', 'fish_3', 'obstacle_1', 'robot']\n",
"\n",
"All poses\n",
- "[[[1.36782631e-01 4.68791187e-01 2.42182687e-01 6.48771763e-01]\n",
- " [7.93363988e-01 3.50356251e-01 3.64646018e-01 1.12773582e-01]\n",
- " [2.60495663e-01 8.65413904e-01 2.21576691e-02 6.10984743e-01]\n",
+ "[[[5.20669639e-01 4.58831601e-02 9.51813161e-01 3.06678474e-01]\n",
+ " [4.54089224e-01 4.62401301e-01 7.62699127e-01 6.46753490e-01]\n",
+ " [9.67400968e-01 5.63468635e-01 9.99894381e-01 1.45336846e-02]\n",
" ...\n",
- " [8.34640980e-01 9.05928910e-01 7.33852565e-01 9.64702129e-01]\n",
- " [5.20252772e-02 1.44064710e-01 9.47307721e-02 3.03431451e-01]\n",
- " [1.99740291e-01 3.40426266e-02 5.65072261e-02 4.65648413e-01]]\n",
+ " [8.80278572e-02 3.80126536e-01 9.97331321e-01 7.30081499e-02]\n",
+ " [3.28493923e-01 6.17436647e-01 9.20374036e-01 3.91039193e-01]\n",
+ " [7.53752515e-02 2.74342328e-01 7.84065127e-01 6.20678544e-01]]\n",
"\n",
- " [[2.59539992e-01 3.93728465e-01 9.71068442e-01 6.31185651e-01]\n",
- " [1.83127314e-01 1.43956905e-02 4.26256537e-01 5.80079734e-01]\n",
- " [3.76704991e-01 6.72040820e-01 5.88318594e-02 3.48662198e-01]\n",
+ " [[4.45818096e-01 5.39128423e-01 5.66779137e-01 8.23869765e-01]\n",
+ " [4.38290328e-01 3.78231764e-01 9.88384008e-01 1.51977092e-01]\n",
+ " [1.82629541e-01 8.08078349e-01 8.27510357e-01 5.61450422e-01]\n",
" ...\n",
- " [3.48356485e-01 9.14380550e-01 4.48769242e-01 7.38050520e-01]\n",
- " [6.12327099e-01 1.99107945e-01 8.90928864e-01 2.84884181e-02]\n",
- " [8.27723503e-01 6.57829344e-01 4.65144426e-01 4.01587933e-01]]\n",
+ " [5.48624545e-02 9.00771558e-01 8.00554574e-01 5.99259913e-01]\n",
+ " [8.34412515e-01 2.47002933e-02 8.98045361e-01 4.39902902e-01]\n",
+ " [2.35550269e-01 5.17610013e-01 7.89557755e-01 6.13676250e-01]]\n",
"\n",
- " [[8.43813717e-01 3.53193313e-01 3.37166399e-01 4.36319530e-01]\n",
- " [9.16836739e-01 2.00342074e-01 1.78178921e-01 6.41124010e-01]\n",
- " [4.94625986e-01 2.56477743e-01 3.52547020e-01 7.87709892e-01]\n",
+ " [[4.05882373e-02 9.17375386e-01 9.94780242e-01 1.02040365e-01]\n",
+ " [8.21412623e-01 6.68225110e-01 9.35957074e-01 3.52114081e-01]\n",
+ " [8.17060947e-01 2.38414750e-01 9.85274673e-01 1.70979008e-01]\n",
" ...\n",
- " [5.02124608e-01 6.97787464e-01 2.58715957e-01 2.88078666e-01]\n",
- " [9.08326209e-01 2.46579379e-01 1.59346357e-01 6.96394265e-01]\n",
- " [3.52213830e-01 6.03601038e-02 2.54920900e-01 3.10269982e-01]]\n",
+ " [1.20162942e-01 4.16668624e-01 9.17142212e-01 3.98560166e-01]\n",
+ " [9.19857025e-01 7.85686851e-01 6.58272266e-01 7.52779961e-01]\n",
+ " [8.69306684e-01 5.62790215e-01 9.19795334e-01 3.92398477e-01]]\n",
"\n",
" [[5.00000000e+01 5.00000000e+01 1.00000000e+00 0.00000000e+00]\n",
" [ nan nan nan nan]\n",
@@ -46,38 +104,38 @@
" [ nan nan nan nan]\n",
" [ nan nan nan nan]]\n",
"\n",
- " [[5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]\n",
- " [5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]\n",
- " [5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]\n",
+ " [[5.00000000e+01 5.00000000e+01 1.00000000e+00 0.00000000e+00]\n",
+ " [5.00000000e+01 5.00000000e+01 1.00000000e+00 0.00000000e+00]\n",
+ " [5.00000000e+01 5.00000000e+01 1.00000000e+00 0.00000000e+00]\n",
" ...\n",
- " [5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]\n",
- " [5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]\n",
- " [5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]]]\n",
+ " [5.00000000e+01 5.00000000e+01 1.00000000e+00 0.00000000e+00]\n",
+ " [5.00000000e+01 5.00000000e+01 1.00000000e+00 0.00000000e+00]\n",
+ " [5.00000000e+01 5.00000000e+01 1.00000000e+00 0.00000000e+00]]]\n",
"\n",
"Fish poses\n",
- "[[[0.13678263 0.46879119 0.24218269 0.64877176]\n",
- " [0.79336399 0.35035625 0.36464602 0.11277358]\n",
- " [0.26049566 0.8654139 0.02215767 0.61098474]\n",
+ "[[[0.52066964 0.04588316 0.95181316 0.30667847]\n",
+ " [0.45408922 0.4624013 0.76269913 0.64675349]\n",
+ " [0.96740097 0.56346864 0.99989438 0.01453368]\n",
" ...\n",
- " [0.83464098 0.90592891 0.73385257 0.96470213]\n",
- " [0.05202528 0.14406471 0.09473077 0.30343145]\n",
- " [0.19974029 0.03404263 0.05650723 0.46564841]]\n",
+ " [0.08802786 0.38012654 0.99733132 0.07300815]\n",
+ " [0.32849392 0.61743665 0.92037404 0.39103919]\n",
+ " [0.07537525 0.27434233 0.78406513 0.62067854]]\n",
"\n",
- " [[0.25953999 0.39372846 0.97106844 0.63118565]\n",
- " [0.18312731 0.01439569 0.42625654 0.58007973]\n",
- " [0.37670499 0.67204082 0.05883186 0.3486622 ]\n",
+ " [[0.4458181 0.53912842 0.56677914 0.82386976]\n",
+ " [0.43829033 0.37823176 0.98838401 0.15197709]\n",
+ " [0.18262954 0.80807835 0.82751036 0.56145042]\n",
" ...\n",
- " [0.34835649 0.91438055 0.44876924 0.73805052]\n",
- " [0.6123271 0.19910794 0.89092886 0.02848842]\n",
- " [0.8277235 0.65782934 0.46514443 0.40158793]]\n",
+ " [0.05486245 0.90077156 0.80055457 0.59925991]\n",
+ " [0.83441252 0.02470029 0.89804536 0.4399029 ]\n",
+ " [0.23555027 0.51761001 0.78955775 0.61367625]]\n",
"\n",
- " [[0.84381372 0.35319331 0.3371664 0.43631953]\n",
- " [0.91683674 0.20034207 0.17817892 0.64112401]\n",
- " [0.49462599 0.25647774 0.35254702 0.78770989]\n",
+ " [[0.04058824 0.91737539 0.99478024 0.10204037]\n",
+ " [0.82141262 0.66822511 0.93595707 0.35211408]\n",
+ " [0.81706095 0.23841475 0.98527467 0.17097901]\n",
" ...\n",
- " [0.50212461 0.69778746 0.25871596 0.28807867]\n",
- " [0.90832621 0.24657938 0.15934636 0.69639426]\n",
- " [0.35221383 0.0603601 0.2549209 0.31026998]]]\n",
+ " [0.12016294 0.41666862 0.91714221 0.39856017]\n",
+ " [0.91985703 0.78568685 0.65827227 0.75277996]\n",
+ " [0.86930668 0.56279022 0.91979533 0.39239848]]]\n",
"\n",
"File structure\n",
" format_url:\thttps://git.imp.fu-berlin.de/bioroboticslab/robofish/track_format/-/releases/1.0\n",
@@ -114,64 +172,16 @@
}
],
"source": [
- "#! /usr/bin/env python3\n",
- "\n",
- "import robofish.io\n",
- "from robofish.io import utils\n",
- "import numpy as np\n",
- "\n",
- "\n",
- "def create_example_file(path):\n",
- " # Create a new io file object with a 100x100cm world\n",
- " sf = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25.0)\n",
- "\n",
- " # create a simple obstacle, fixed in place, fixed outline\n",
- " obstacle_outline = [[[-10, -10], [-10, 0], [0, 0], [0, -10]]]\n",
- " obstacle_name = sf.create_entity(\n",
- " \"obstacle\", positions=[[50, 50]], orientations=[[0]], outlines=obstacle_outline\n",
- " )\n",
- "\n",
- " # create a robofish with 1000 timesteps. If we would not give a name, the name would be generated to be robot_1.\n",
- " robofish_timesteps = 1000\n",
- " robofish_poses = np.ones((robofish_timesteps, 4)) * 50\n",
- " robot = sf.create_entity(\"robot\", robofish_poses, name=\"robot\")\n",
- "\n",
- " # create multiple fishes with timestamps. Since we don't specify names, but only the type \"fish\" the fishes will be named [\"fish_1\", \"fish_2\", \"fish_3\"]\n",
- " agents = 3\n",
- " timesteps = 1000\n",
- " # timestamps = np.linspace(0, timesteps + 1, timesteps)\n",
- " agent_poses = np.random.random((agents, timesteps, 4))\n",
- "\n",
- " fishes = sf.create_multiple_entities(\"fish\", agent_poses)\n",
- "\n",
- " # This would throw an exception if the file was invalid\n",
- " sf.validate()\n",
- "\n",
- " # Save file validates aswell\n",
- "\n",
- " sf.save_as(path)\n",
- "\n",
- " # Closing and opening files (just for demonstration)\n",
- " sf.close()\n",
- " sf = robofish.io.File(path=path)\n",
- "\n",
- " print(\"\\nEntity Names\")\n",
- " print(sf.entity_names)\n",
- "\n",
- " # Get an array with all poses. As the length of poses varies per agent, it is filled up with nans.\n",
- " print(\"\\nAll poses\")\n",
- " print(sf.entity_poses)\n",
- "\n",
- " print(\"\\nFish poses\")\n",
- " print(sf.select_entity_poses(lambda e: e.category == \"fish\"))\n",
- "\n",
- " print(\"\\nFile structure\")\n",
- " print(sf)\n",
- "\n",
- "\n",
"if __name__ == \"__main__\":\n",
- " create_example_file(\"example.hdf5\")\n"
+ " create_example_file(\"example.hdf5\")"
]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
}
],
"metadata": {
diff --git a/examples/example_basic.py b/examples/example_basic.py
index dec8e3be1c7997b33b36f9868f0df8b0c6c3fbe6..34e092296f6edde6301a13623c15f77a46ddb70a 100755
--- a/examples/example_basic.py
+++ b/examples/example_basic.py
@@ -1,56 +1,53 @@
-#! /usr/bin/env python3
-
import robofish.io
-from robofish.io import utils
import numpy as np
def create_example_file(path):
# Create a new io file object with a 100x100cm world
- sf = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25.0)
+ f = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25.0)
# create a simple obstacle, fixed in place, fixed outline
obstacle_outline = [[[-10, -10], [-10, 0], [0, 0], [0, -10]]]
- obstacle_name = sf.create_entity(
+ obstacle_name = f.create_entity(
"obstacle", positions=[[50, 50]], orientations=[[0]], outlines=obstacle_outline
)
# create a robofish with 1000 timesteps. If we would not give a name, the name would be generated to be robot_1.
robofish_timesteps = 1000
- robofish_poses = np.ones((robofish_timesteps, 4)) * 50
- robot = sf.create_entity("robot", robofish_poses, name="robot")
+ robofish_poses = np.tile([50, 50, 1, 0], (robofish_timesteps, 1))
+ robot = f.create_entity("robot", name="robot", poses=robofish_poses)
# create multiple fishes with timestamps. Since we don't specify names, but only the type "fish" the fishes will be named ["fish_1", "fish_2", "fish_3"]
agents = 3
timesteps = 1000
# timestamps = np.linspace(0, timesteps + 1, timesteps)
- agent_poses = np.random.random((agents, timesteps, 4))
+ agent_poses = np.random.random((agents, timesteps, 3))
- fishes = sf.create_multiple_entities("fish", agent_poses)
+ fishes = f.create_multiple_entities("fish", agent_poses)
# This would throw an exception if the file was invalid
- sf.validate()
+ f.validate()
# Save file validates aswell
+ f.save_as(path)
- sf.save_as(path)
-
- # Closing and opening files (just for demonstration)
- sf.close()
- sf = robofish.io.File(path=path)
+ # Closing and opening files (just for demonstration). When opening with r+, we can read and write afterwards.
+ f.close()
+ f = robofish.io.File(path, "r+")
print("\nEntity Names")
- print(sf.entity_names)
+ print(f.entity_names)
# Get an array with all poses. As the length of poses varies per agent, it is filled up with nans.
print("\nAll poses")
- print(sf.entity_poses)
+ print(f.entity_poses)
+ # Select all entities with the category fish
print("\nFish poses")
- print(sf.select_entity_poses(lambda e: e.category == "fish"))
+ print(f.select_entity_poses(lambda e: e.category == "fish"))
- print("\nFile structure")
- print(sf)
+ print("\nFinal file")
+ print(f)
if __name__ == "__main__":
diff --git a/examples/example_readme.py b/examples/example_readme.py
index f489958f1fd994dce6c19c46cd56bb7aab1b16f2..62df2336f89281a0d9306428839e9aee2921ae4b 100644
--- a/examples/example_readme.py
+++ b/examples/example_readme.py
@@ -1,35 +1,38 @@
import robofish.io
import numpy as np
-from pathlib import Path
def create_example_file(path):
- # By using the context, the file will be automatically validated
- with robofish.io.File(path, "w", world_size_cm=[100, 100], frequency_hz=25.0) as f:
- f.attrs["experiment_setup"] = "This is a simple example with made up data."
-
- # Create a single robot with 30 timesteps
- # positions are passed separately
- # orientations are passed as with two columns -> orientation_x and orientation_y
- f.create_entity(
- category="robot",
- name="robot",
- positions=np.zeros((100, 2)),
- orientations=np.ones((100, 2)) * [0, 1],
- )
-
- # Create fishes with 30 poses (x, y, orientation_rad)
- poses = np.zeros((100, 3))
- poses[:, 0] = np.arange(-50, 50)
- poses[:, 1] = np.arange(-50, 50)
- poses[:, 2] = np.arange(0, 2 * np.pi, step=2 * np.pi / 100)
- fish = f.create_entity("fish", poses=poses)
- fish.attrs["species"] = "My rotating spaghetti fish"
- fish.attrs["fish_standard_length_cm"] = 10
-
- # Show and save the file
- print(f)
- print("Poses Shape: ", f.entity_poses.shape)
+ # Create a new robofish io file
+ f = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25.0)
+ f.attrs["experiment_setup"] = "This is a simple example with made up data."
+
+ # Create a new robot entity. Positions and orientations are passed
+ # separately in this example. Since the orientations have two columns,
+ # unit vectors are assumed (orientation_x, orientation_y)
+ f.create_entity(
+ category="robot",
+ name="robot",
+ positions=np.zeros((100, 2)),
+ orientations=np.ones((100, 2)) * [0, 1],
+ )
+
+ # Create a new fish entity.
+ # In this case, we pass positions and orientations together (x, y, rad).
+ # Since it is a 3 column array, orientations in radiants are assumed.
+ poses = np.zeros((100, 3))
+ poses[:, 0] = np.arange(-50, 50)
+ poses[:, 1] = np.arange(-50, 50)
+ poses[:, 2] = np.arange(0, 2 * np.pi, step=2 * np.pi / 100)
+ fish = f.create_entity("fish", poses=poses)
+ fish.attrs["species"] = "My rotating spaghetti fish"
+ fish.attrs["fish_standard_length_cm"] = 10
+
+ # Show and save the file
+ print(f)
+ print("Poses Shape: ", f.entity_poses.shape)
+
+ f.save_as(path)
if __name__ == "__main__":
diff --git a/setup.py b/setup.py
index 5be2fe4573c17f9dbb776058058ea0e38c4674aa..552f54e96c461e588672a3238c82b98cee1b8030 100644
--- a/setup.py
+++ b/setup.py
@@ -14,9 +14,15 @@ entry_points = {
]
}
+
def source_version():
version_parts = (
- run(["git", "describe", "--tags", "--dirty"], check=True, stdout=PIPE, encoding="utf-8")
+ run(
+ ["git", "describe", "--tags", "--dirty"],
+ check=True,
+ stdout=PIPE,
+ encoding="utf-8",
+ )
.stdout.strip()
.split("-")
)
@@ -36,12 +42,13 @@ def source_version():
return version
+
setup(
name="robofish-io",
version=source_version(),
author="",
author_email="",
- install_requires=["h5py>=3", "numpy", "seaborn", "pandas", "deprecation"],
+ install_requires=["h5py>=2.10.0", "numpy", "seaborn", "pandas", "deprecation"],
classifiers=[
"Development Status :: 3 - Alpha",
"Intended Audience :: Science/Research",
diff --git a/src/robofish/io/entity.py b/src/robofish/io/entity.py
index 8ef557c3d7d0bdcdd010f47055a121ca3452114f..669ac1746ab15dd5c24e6eae1b6986bf97c6a49b 100644
--- a/src/robofish/io/entity.py
+++ b/src/robofish/io/entity.py
@@ -30,6 +30,12 @@ class Entity(h5py.Group):
poses, positions, orientations, outlines
)
+ assert poses is None or (poses.ndim == 2 and poses.shape[1] in [3, 4])
+ assert positions is None or (positions.ndim == 2 and positions.shape[1] == 2)
+ assert orientations is None or (
+ orientations.ndim == 2 and orientations.shape[1] in [1, 2]
+ )
+
# If no name is given, create one from type and an id
if name is None:
i = 1
@@ -53,6 +59,10 @@ class Entity(h5py.Group):
@classmethod
def convert_rad_to_vector(cla, orientations_rad):
+ if min(orientations_rad) < 0 or max(orientations_rad) > 2 * np.pi:
+ logging.warning(
+ "Converting orientations, from a bigger range than [0, 2 * pi]. When passing the orientations, they are assumed to be in radiants."
+ )
ori_rad = utils.np_array(orientations_rad)
assert ori_rad.shape[1] == 1
ori_vec = np.empty((ori_rad.shape[0], 2))
@@ -98,7 +108,7 @@ class Entity(h5py.Group):
else:
if poses is not None:
- assert poses.shape[1] == 3 or poses.shape[1] == 4
+ assert poses.shape[1] in [3, 4]
positions = poses[:, :2]
orientations = poses[:, 2:]
if orientations is not None and orientations.shape[1] == 1:
@@ -107,9 +117,10 @@ class Entity(h5py.Group):
positions = self.create_dataset(
"positions", data=positions, dtype=np.float32
)
- orientations = self.create_dataset(
- "orientations", data=orientations, dtype=np.float32
- )
+ if orientations is not None:
+ orientations = self.create_dataset(
+ "orientations", data=orientations, dtype=np.float32
+ )
if sampling is not None:
positions.attrs["sampling"] = sampling
@@ -121,6 +132,9 @@ class Entity(h5py.Group):
@property
def orientations(self):
+ if not "orientations" in self:
+ # If no orientation is given, the default direction is to the right
+ return np.tile([1, 0], (self.positions.shape[0], 1))
return self["orientations"]
@property
diff --git a/src/robofish/io/file.py b/src/robofish/io/file.py
index 669c05c0bc3e019b099e4357e69ae07534318862..e4798c809fc28fe367e7b8198065622dcdbc341a 100644
--- a/src/robofish/io/file.py
+++ b/src/robofish/io/file.py
@@ -208,14 +208,19 @@ class File(h5py.File):
)
if default:
- self.default_sampling = name
- self["samplings"].attrs["default"] = self.default_sampling
+ self["samplings"].attrs["default"] = name
return name
@property
def world_size(self):
return self.attrs["world_size_cm"]
+ @property
+ def default_sampling(self):
+ if "default" in self["samplings"].attrs:
+ return self["samplings"].attrs["default"]
+ return None
+
@property
def frequency(self):
# NOTE: Only works if default sampling availabe and specified with frequency_hz.
@@ -245,11 +250,10 @@ class File(h5py.File):
Name of the created entity
"""
- if sampling is None:
- if not hasattr(self, "default_sampling"):
- raise Exception(
- "There was no sampling specified, when creating the file, nor when creating the entity."
- )
+ if sampling is None and self.default_sampling is None:
+ raise Exception(
+ "There was no sampling specified, when creating the file, nor when creating the entity."
+ )
entity = robofish.io.Entity.create_entity(
self["entities"],
@@ -285,18 +289,18 @@ class File(h5py.File):
"""
assert poses.ndim == 3
- assert poses.shape[2] == 4
- n = poses.shape[0]
+ assert poses.shape[2] in [3, 4]
+ agents = poses.shape[0]
timesteps = poses.shape[1]
- returned_names = []
+ entity_names = []
- for i in range(n):
+ for i in range(agents):
e_name = None if names is None else names[i]
e_outline = (
outlines if outlines is None or outlines.ndim == 3 else outlines[i]
)
- returned_names.append(
+ entity_names.append(
self.create_entity(
category=category,
sampling=sampling,
@@ -305,7 +309,7 @@ class File(h5py.File):
outlines=e_outline,
)
)
- return returned_names
+ return entity_names
@property
def entity_names(self) -> Iterable[str]:
@@ -327,8 +331,13 @@ class File(h5py.File):
def entity_poses(self):
return self.select_entity_poses(None)
- def select_entity_poses(self, predicate=None) -> Iterable:
- """ Select an array of the poses of entities
+ @property
+ def entity_poses_rad(self):
+ return self.select_entity_poses(None, rad=True)
+
+ def select_entity_poses(self, predicate=None, rad=False) -> Iterable:
+ """ TODO: Rework
+ Select an array of the poses of entities
If no name or category is specified, all entities will be selected.
@@ -346,7 +355,8 @@ class File(h5py.File):
max_timesteps = max([0] + [e.positions.shape[0] for e in entities])
# Initialize poses output array
- poses_output = np.empty((len(entities), max_timesteps, 4))
+ pose_len = 3 if rad else 4
+ poses_output = np.empty((len(entities), max_timesteps, pose_len))
poses_output[:] = np.nan
# Fill poses output array
@@ -361,7 +371,7 @@ class File(h5py.File):
raise Exception(
"Multiple samplings found, preventing return of a single array."
)
- poses = entity.poses
+ poses = entity.poses_rad if rad else entity.poses
poses_output[i][: poses.shape[0]] = poses
i += 1
return poses_output
diff --git a/src/robofish/io/validation.py b/src/robofish/io/validation.py
index 0718d2d95b5685baa46147f3f390179c0b8a16f5..a1bde527f16a2b28431c6b1148a4ecfec50d2354 100644
--- a/src/robofish/io/validation.py
+++ b/src/robofish/io/validation.py
@@ -200,7 +200,9 @@ def validate(iofile: File, strict_validate: bool = True) -> (bool, str):
if positions.shape[0] > 0:
# validate range of poses
- validate_poses_range(iofile, positions, e_name)
+ validate_positions_range(
+ iofile.attrs["world_size_cm"], positions, e_name
+ )
if "orientations" in entity:
assert_validate(
@@ -228,6 +230,8 @@ def validate(iofile: File, strict_validate: bool = True) -> (bool, str):
e_name,
)
+ validate_orientations_length(orientations, e_name)
+
# outlines
if "outlines" in entity:
outlines = entity["outlines"]
@@ -291,37 +295,48 @@ def validate(iofile: File, strict_validate: bool = True) -> (bool, str):
return (True, "")
-def validate_poses_range(iofile, poses, e_name):
- # Poses which are just a bit over the world edge are fine
+def validate_positions_range(world_size, positions, e_name):
+ # positions which are just a bit over the world edge are fine
error_allowance = 1.01
allowed_x = [
- -1 * iofile.attrs["world_size_cm"][0] * error_allowance / 2,
- iofile.attrs["world_size_cm"][0] * error_allowance / 2,
+ -1 * world_size[0] * error_allowance / 2,
+ world_size[0] * error_allowance / 2,
]
- real_x = [poses[:, 0].min(), poses[:, 0].max()]
+ real_x = [positions[:, 0].min(), positions[:, 0].max()]
allowed_y = [
- -1 * iofile.attrs["world_size_cm"][1] * error_allowance / 2.0,
- iofile.attrs["world_size_cm"][1] * error_allowance / 2.0,
+ -1 * world_size[1] * error_allowance / 2.0,
+ world_size[1] * error_allowance / 2.0,
]
- real_y = [poses[:, 1].min(), poses[:, 1].max()]
+ real_y = [positions[:, 1].min(), positions[:, 1].max()]
assert_validate(
allowed_x[0] <= real_x[0] and real_x[1] <= allowed_x[1],
- "Poses of x axis were not in range. The allowed range is [%.1f, %.1f], which was [%.1f, %.1f] in the poses"
+ "Positions of x axis were not in range. The allowed range is [%.1f, %.1f], which was [%.1f, %.1f] in the Positions"
% (allowed_x[0], allowed_x[1], real_x[0], real_x[1]),
e_name,
)
assert_validate(
allowed_y[0] <= real_y[0] and real_y[1] <= allowed_y[1],
- "Poses of y axis were not in range. The allowed range is [%.1f, %.1f], which was [%.1f, %.1f] in the poses"
+ "Positions of y axis were not in range. The allowed range is [%.1f, %.1f], which was [%.1f, %.1f] in the Positions"
% (allowed_y[0], allowed_y[1], real_y[0], real_y[1]),
e_name,
)
+def validate_orientations_length(orientations, e_name):
+ ori_lengths = np.linalg.norm(orientations, axis=1)
+
+ assert_validate(
+ np.isclose(ori_lengths, 1).all(),
+ "The orientation vectors were not unit vectors. Their length was in the range [%.2f, %.2f] when it should be 1"
+ % (min(ori_lengths), max(ori_lengths)),
+ e_name,
+ )
+
+
def validate_iso8601(str_val: str) -> bool:
"""This function validates strings to match the ISO8601 format.
diff --git a/tests/robofish/evaluate/test_app_evaluate.py b/tests/robofish/evaluate/test_app_evaluate.py
index 58ca278882b1756830fd66b7a37a4cb823d8199a..2a7fe486a95c961f41f591ea7c8ab533db6b2ccf 100644
--- a/tests/robofish/evaluate/test_app_evaluate.py
+++ b/tests/robofish/evaluate/test_app_evaluate.py
@@ -22,7 +22,7 @@ def test_app_validate():
self.names = None
self.save_path = graphics_out
- # TODO: Get rid of deprecated get_poses function
+ # TODO: Get rid of deprecation
with pytest.warns(DeprecationWarning):
app.evaluate(DummyArgs("speed"))
graphics_out.unlink()
diff --git a/tests/robofish/io/test_examples.py b/tests/robofish/io/test_examples.py
index 1d0379fb1b06448e5f733c3690ff48a4f623592c..c81b1eed99221e9d92a82f0d354352fa869cfbae 100644
--- a/tests/robofish/io/test_examples.py
+++ b/tests/robofish/io/test_examples.py
@@ -1,12 +1,13 @@
import robofish.io
from robofish.io import utils
from pathlib import Path
+from testbook import testbook
import sys
sys.path.append(str(utils.full_path(__file__, "../../../examples/")))
-
+ipynb_path = utils.full_path(__file__, "../../../examples/example_basic.ipynb")
path = utils.full_path(__file__, "../../../examples/tmp_example.hdf5")
if path.exists():
path.unlink()
@@ -24,3 +25,21 @@ def test_example_basic():
example_basic.create_example_file(path)
path.unlink()
+
+
+# This test can be executed manually. The CI/CD System has issues with testbook.
+def manual_test_example_basic_ipynb():
+ # Executing the notebook should not lead to an exception
+ with testbook(str(ipynb_path), execute=True) as tb:
+ pass
+ # tb.ref("create_example_file")(path)
+ # path.unlink()
+
+
+if __name__ == "__main__":
+ print("example_readme.py")
+ test_example_readme()
+ print("example_basic.py")
+ test_example_basic()
+ print("example_basic.ipynb")
+ manual_test_example_basic_ipynb()
diff --git a/tests/robofish/io/test_file.py b/tests/robofish/io/test_file.py
index e19031ea8008470df9560a2e685b8716826c6e11..31c54bc8382f82aa6376af26f08fcafe257f619a 100644
--- a/tests/robofish/io/test_file.py
+++ b/tests/robofish/io/test_file.py
@@ -8,6 +8,8 @@ import datetime
import sys
import logging
+LOGGER = logging.getLogger(__name__)
+
valid_file_path = utils.full_path(__file__, "../../resources/valid.hdf5")
created_by_test_path = utils.full_path(__file__, "../../resources/created_by_test.hdf5")
created_by_test_path_2 = utils.full_path(
@@ -42,6 +44,7 @@ def test_missing_attribute():
def test_single_entity_monotonic_step():
sf = robofish.io.File(world_size_cm=[100, 100], frequency_hz=(1000 / 40))
test_poses = np.ones(shape=(10, 4))
+ test_poses[:, 3] = 0 # All Fish pointing right
sf.create_entity("robofish", poses=test_poses)
sf.create_entity("object_without_poses")
print(sf)
@@ -53,6 +56,7 @@ def test_single_entity_monotonic_time_points_us():
world_size_cm=[100, 100], monotonic_time_points_us=np.ones(10)
)
test_poses = np.ones(shape=(10, 4))
+ test_poses[:, 3] = 0 # All Fish pointing right
sf.create_entity("robofish", poses=test_poses)
print(sf)
sf.validate()
@@ -64,7 +68,7 @@ def test_multiple_entities():
poses = np.zeros((agents, timesteps, 4))
poses[1] = 1
- poses[2] = 2
+ poses[:, :, 2:] = [1, 0] # All agents point to the right
m_points = np.arange(timesteps)
@@ -95,9 +99,9 @@ def test_multiple_entities():
assert (returned_poses == poses[:1]).all()
# Insert some random obstacles
- returned_names = sf.create_multiple_entities(
- "obstacle", poses=np.random.random((agents, timesteps, 4))
- )
+ obstacles = 3
+ obs_poses = np.random.random((agents, 1, 3))
+ returned_names = sf.create_multiple_entities("obstacle", poses=obs_poses)
# Obstacles should not be returned when only fish are selected
returned_poses = sf.select_entity_poses(lambda e: e.category == "fish")
assert (returned_poses == poses).all()
@@ -115,12 +119,6 @@ def test_multiple_entities():
monotonic_time_points_us=m_points, calendar_time_points=c_points
)
- try:
- sf.create_sampling(frequency_hz=25, monotonic_time_points_us=m_points)
- raise Exception("This sampling should have created an error")
- except:
- pass
-
returned_names = sf.create_multiple_entities(
"fish", poses, outlines=outlines, sampling=new_sampling
)
@@ -129,6 +127,9 @@ def test_multiple_entities():
# pass an poses array in separate parts (positions, orientations) and retrieve it with poses.
poses_arr = np.random.random((100, 4))
+ poses_arr[:, 2:] /= np.atleast_2d(
+ np.linalg.norm(poses_arr[:, 2:], axis=1)
+ ).T # Normalization
position_orientation_fish = sf.create_entity(
"fish", positions=poses_arr[:, :2], orientations=poses_arr[:, 2:]
)
@@ -138,6 +139,15 @@ def test_multiple_entities():
return sf
+def test_broken_sampling(caplog):
+ sf = robofish.io.File(world_size_cm=[10, 10])
+ caplog.set_level(logging.ERROR)
+ broken_sampling = sf.create_sampling(
+ name="broken sampling", frequency_hz=25, monotonic_time_points_us=np.ones((100))
+ )
+ assert "ERROR" in caplog.text
+
+
def test_deprecated_get_poses():
f = test_multiple_entities()
with pytest.warns(DeprecationWarning):
@@ -146,6 +156,29 @@ def test_deprecated_get_poses():
assert f.get_poses(names="fish_1").shape[0] == 1
+def test_entity_poses_rad(caplog):
+ with robofish.io.File(world_size_cm=[100, 100], frequency_hz=25) as f:
+ # Create an entity, using radiants
+ f.create_entity("fish", poses=np.ones((100, 3)))
+
+ # Read the poses of the file as radiants
+ np.testing.assert_almost_equal(f.entity_poses_rad, np.ones((1, 100, 3)))
+
+ caplog.set_level(logging.WARNING)
+ # Passing orientations, which are bigger than 2 pi
+ f.create_entity("fish", poses=np.ones((100, 3)) * 50)
+ assert "WARNING" in caplog.text
+
+
+def test_entity_positions_no_orientation():
+ with robofish.io.File(world_size_cm=[100, 100], frequency_hz=25) as f:
+ # Create an entity, using radiants
+ f.create_entity("fish", positions=np.ones((100, 2)))
+
+ assert f.entity_poses.shape == (1, 100, 4)
+ assert (f.entity_poses[:, :] == np.array([1, 1, 1, 0])).all()
+
+
def test_load_validate():
sf = robofish.io.File(path=valid_file_path)
sf.validate()
@@ -173,6 +206,12 @@ def test_loading_saving():
# After saving, the file should still be accessible and valid
sf.validate()
+ # Open the file again and add another entity
+ sf = robofish.io.File(created_by_test_path, "r+")
+ entity = sf.create_entity("fish", positions=np.ones((100, 2)))
+ sf.entity_poses
+ entity.poses
+
def test_validate_created_file_after_reloading():
sf = robofish.io.File(created_by_test_path)
@@ -182,8 +221,9 @@ def test_validate_created_file_after_reloading():
# Cleanup test. The z in the name makes sure, that it is executed last in main
def test_z_cleanup():
""" This cleans up after all tests and removes all test artifacts """
- created_by_test_path.unlink()
- created_by_test_path_2.unlink()
+ for f in [created_by_test_path, created_by_test_path_2]:
+ if f.exists():
+ f.unlink()
if __name__ == "__main__":