From b0ea2152f5f26c34007f5ff6390eecb8770bb26b Mon Sep 17 00:00:00 2001
From: Andi Gerken <andi.gerken@gmail.com>
Date: Wed, 30 Mar 2022 14:01:45 +0000
Subject: [PATCH] Changed storage of calculated data from implicit to explicit.
---
setup.py | 3 +-
src/robofish/io/__init__.py | 6 --
src/robofish/io/app.py | 45 ++++++++-
src/robofish/io/entity.py | 157 ++++++++++++++++++-------------
src/robofish/io/file.py | 46 ++++++++-
tests/resources/nan_test.hdf5 | Bin 12296 -> 15576 bytes
tests/resources/valid_1.hdf5 | Bin 65536 -> 23272 bytes
tests/resources/valid_2.hdf5 | Bin 15672 -> 22488 bytes
tests/robofish/io/test_app_io.py | 10 +-
9 files changed, 186 insertions(+), 81 deletions(-)
diff --git a/setup.py b/setup.py
index 48573d8..a9ebe9c 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,8 @@ entry_points = {
"robofish-io-validate=robofish.io.app:validate",
"robofish-io-print=robofish.io.app:print_file",
"robofish-io-render=robofish.io.app:render",
- "robofish-io-clear-calculated-data=robofish.io.app:clear_calculated_data",
+ # "robofish-io-clear-calculated-data=robofish.io.app:clear_calculated_data",
+ "robofish-io-update-calculated-data=robofish.io.app:update_calculated_data",
# TODO: This should be called robofish-evaluate which is not possible because of the package name (guess) ask moritz
"robofish-io-evaluate=robofish.evaluate.app:evaluate",
]
diff --git a/src/robofish/io/__init__.py b/src/robofish/io/__init__.py
index b14b319..5b054c2 100644
--- a/src/robofish/io/__init__.py
+++ b/src/robofish/io/__init__.py
@@ -20,9 +20,3 @@ import robofish.io.app
if not ((3, 7) <= sys.version_info < (4, 0)):
logging.warning("Unsupported Python version")
-
-warn_when_unable_to_store = True
-
-
-def disable_warning_when_unable_to_store():
- robofish.io.warn_when_unable_to_store = False
diff --git a/src/robofish/io/app.py b/src/robofish/io/app.py
index 15b6ebe..c6a9385 100644
--- a/src/robofish/io/app.py
+++ b/src/robofish/io/app.py
@@ -15,6 +15,7 @@ from robofish.io import utils
import argparse
import logging
+import warnings
def print_file(args=None):
@@ -53,9 +54,9 @@ def print_file(args=None):
return not valid
-def clear_calculated_data(args=None):
+def update_calculated_data(args=None):
parser = argparse.ArgumentParser(
- description="This function clears calculated data from robofish.io files."
+ description="This function updates all calculated data from files."
)
parser.add_argument(
@@ -76,8 +77,42 @@ def clear_calculated_data(args=None):
for fp in files:
print(f"File {fp}")
- with robofish.io.File(fp, "r+") as f:
- f.clear_calculated_data()
+ try:
+ with robofish.io.File(fp, "r+", validate_poses_hash=False) as f:
+ f.update_calculated_data(verbose=True)
+ except Exception as e:
+ warnings.warn(f"The file {fp} could not be updated.")
+ print(e)
+
+
+# This should not be neccessary since the data will always have the calculated data by default.
+# def clear_calculated_data(args=None):
+# parser = argparse.ArgumentParser(
+# description="This function clears calculated data from robofish.io files."
+# )
+
+# parser.add_argument(
+# "path",
+# type=str,
+# nargs="+",
+# help="The path to one or multiple files and/or folders.",
+# )
+# if args is None:
+# args = parser.parse_args()
+
+# files_per_path = utils.get_all_files_from_paths(args.path)
+# files = [
+# f for f_in_path in files_per_path for f in f_in_path
+# ] # Concatenate all files to one list
+
+# assert len(files) > 0, f"No files found in path {args.path}."
+
+# for fp in files:
+# print(f"File {fp}")
+# with robofish.io.File(
+# fp, "r+", validate_poses_hash=False, store_calculated_data=False
+# ) as f:
+# f.clear_calculated_data()
def validate(args=None):
@@ -162,7 +197,7 @@ def render(args=None):
default_options = {
"linewidth": 2,
- "speedup": 4,
+ "speedup": 1,
"trail": 100,
"entity_scale": 0.2,
"fixed_view": False,
diff --git a/src/robofish/io/entity.py b/src/robofish/io/entity.py
index fb0b1a2..3375f37 100644
--- a/src/robofish/io/entity.py
+++ b/src/robofish/io/entity.py
@@ -60,6 +60,8 @@ class Entity(h5py.Group):
if outlines is not None:
entity.create_outlines(outlines, sampling)
+ entity.update_calculated_data()
+
return entity
@classmethod
@@ -141,36 +143,6 @@ class Entity(h5py.Group):
return np.tile([0, 1], (self.positions.shape[0], 1))
return self["orientations"]
- @property
- def orientations_rad(self):
- # If actions_speeds_turns does not exist yet or the poses hash is not correct
- if (
- "calculated_orientations_rad" not in self
- or "poses_hash" not in self.attrs
- or self.poses_hash != self.attrs["poses_hash"]
- ):
-
- ori_rad = utils.limit_angle_range(
- np.arctan2(self.orientations[:, 1], self.orientations[:, 0]),
- _range=(0, 2 * np.pi),
- )[:, np.newaxis]
-
- try:
-
- self.attrs["poses_hash"] = self.poses_hash
- self["calculated_orientations_rad"] = ori_rad.astype(np.float64)
- except RuntimeError as e:
- if robofish.io.warn_when_unable_to_store:
- print(
- "Trying to store calculated orientations_rad in file to reuse it but the file was opened as read-only.\n"
- "If you open the file with mode 'r+' (or 'w' if it is still open from creation time) the information can be stored and reused.\n"
- "To disable this message execute robofish.io.disable_warning_when_unable_to_store().\n"
- )
- else:
- ori_rad = self["calculated_orientations_rad"]
-
- return ori_rad
-
@property
@deprecation.deprecated(
deprecated_in="0.2",
@@ -220,11 +192,19 @@ class Entity(h5py.Group):
@property
def poses_hash(self):
+ # The hash of h5py datasets changes each time the file is reopened.
+ # Also the hash of casting the array to bytes and calculating the hash changes.
+ def npsumhash(a):
+ return hash(np.nansum(a))
+
if "orientations" in self:
- h = (hash(self["positions"]) + hash(self["orientations"])) // 2
+ h = (npsumhash(self["positions"]) + npsumhash(self["orientations"])) // 2
+ elif "positions" in self:
+ print("We found positions")
+ h = npsumhash(self["positions"])
else:
- h = hash(self["positions"])
- return int(h)
+ h = 0
+ return h
@property
def poses(self):
@@ -267,8 +247,59 @@ class Entity(h5py.Group):
turn = utils.limit_angle_range(diff[:, 2], _range=(-np.pi, np.pi))
return np.stack([speed, turn], axis=-1)
- @property
- def actions_speeds_turns(self):
+ def update_calculated_data(self, verbose=False, force_update=False):
+ if (
+ "poses_hash" not in self.attrs
+ or self.attrs["poses_hash"] != self.poses_hash
+ or "calculated_orientations_rad" not in self
+ or "calculated_actions_speeds_turns" not in self
+ or "unfinished_calculations" in self.attrs
+ or force_update
+ ):
+ try:
+ self.attrs["poses_hash"] = self.poses_hash
+ self.attrs["unfinished_calculations"] = True
+ if "orientations" in self:
+ ori_rad = self.calculate_orientations_rad()
+ if "calculated_orientations_rad" in self:
+ del self["calculated_orientations_rad"]
+ self["calculated_orientations_rad"] = ori_rad.astype(np.float64)
+
+ speeds_turns = self.calculate_actions_speeds_turns()
+ if "calculated_actions_speeds_turns" in self:
+ del self["calculated_actions_speeds_turns"]
+ self["calculated_actions_speeds_turns"] = speeds_turns.astype(
+ np.float64
+ )
+ del self.attrs["unfinished_calculations"]
+
+ if verbose:
+ print(
+ f"Updated calculated data for entity {self.name} with poses_hash {self.poses_hash}"
+ )
+ elif verbose:
+ print(
+ "Since there were no orientations in the data, nothing was calculated."
+ )
+ except RuntimeError as e:
+ print("Trying to update calculated data in a read-only file")
+ raise e
+ else:
+ if verbose:
+ print(
+ f"Nothing to be updated in entity {self.name}. Poses_hash was {self.attrs['poses_hash']}"
+ )
+
+ assert self.attrs["poses_hash"] == self.poses_hash
+
+ def calculate_orientations_rad(self):
+ ori_rad = utils.limit_angle_range(
+ np.arctan2(self.orientations[:, 1], self.orientations[:, 0]),
+ _range=(0, 2 * np.pi),
+ )[:, np.newaxis]
+ return ori_rad
+
+ def calculate_actions_speeds_turns(self):
"""Calculate the speed, turn and from the recorded positions and orientations.
The turn is calculated by the change of orientation between frames.
@@ -278,36 +309,32 @@ class Entity(h5py.Group):
Returns:
An array with shape (number_of_positions -1, 2 (speed in cm/frame, turn in rad/frame).
"""
+ ori = self.orientations
+ ori_rad = self.orientations_rad
+ pos = self.positions
+ turn = utils.limit_angle_range(np.diff(ori_rad, axis=0)[:, 0])
+ pos_diff = np.diff(pos, axis=0)
+ speed = np.array(
+ [np.dot(pos_diff[i], ori[i + 1]) for i in range(pos_diff.shape[0])]
+ )
+ return np.stack([speed, turn], axis=-1)
- # If actions_speeds_turns does not exist yet or the poses hash is not correct
- if (
- "calculated_actions_speeds_turns" not in self
- or "poses_hash" not in self.attrs
- or self.poses_hash != self.attrs["poses_hash"]
- ):
- ori = self.orientations
- ori_rad = self.orientations_rad
- pos = self.positions
- turn = utils.limit_angle_range(np.diff(ori_rad, axis=0)[:, 0])
- pos_diff = np.diff(pos, axis=0)
- speed = np.array(
- [np.dot(pos_diff[i], ori[i + 1]) for i in range(pos_diff.shape[0])]
- )
- actions_speeds_turns = np.stack([speed, turn], axis=-1)
-
- try:
- self.attrs["poses_hash"] = self.poses_hash
- self["calculated_actions_speeds_turns"] = actions_speeds_turns.astype(
- np.float64
- )
- except RuntimeError as e:
- if robofish.io.warn_when_unable_to_store:
- print(
- "Trying to store calculated actions_speeds_turns in file to reuse it but the file was opened as read-only.\n"
- "If you open the file with mode 'r+' (or 'w' if it is still open from creation time) the information can be stored and reused.\n"
- "To disable this message execute robofish.io.disable_warning_when_unable_to_store().\n"
- )
+ @property
+ def actions_speeds_turns(self):
+ if "calculated_actions_speeds_turns" in self:
+ assert (
+ self.attrs["poses_hash"] == self.poses_hash
+ ), f"The calculated poses_hash was not identical to the stored poses_hash. Please update the calculated data after changing positions or orientations with entity.update_calculated_data(). stored hash: {self.attrs['poses_hash']}, calculated hash: {self.poses_hash}."
+ return self["calculated_actions_speeds_turns"]
else:
- actions_speeds_turns = self["calculated_actions_speeds_turns"]
+ return self.calculate_actions_speeds_turns()
- return actions_speeds_turns
+ @property
+ def orientations_rad(self):
+ if "calculated_orientations_rad" in self:
+ assert (
+ self.attrs["poses_hash"] == self.poses_hash
+ ), f"The calculated poses_hash was not identical to the stored poses_hash. Please update the calculated data after changing positions or orientations with entity.update_calculated_data(). stored hash: {self.attrs['poses_hash']}, calculated hash: {self.poses_hash}."
+ return self["calculated_orientations_rad"]
+ else:
+ return self.calculate_orientations_rad()
diff --git a/src/robofish/io/file.py b/src/robofish/io/file.py
index 40097b5..d57c7bf 100644
--- a/src/robofish/io/file.py
+++ b/src/robofish/io/file.py
@@ -75,6 +75,7 @@ class File(h5py.File):
monotonic_time_points_us: Iterable = None,
calendar_time_points: Iterable = None,
open_copy: bool = False,
+ validate_poses_hash: bool = True,
):
"""Create a new RoboFish Track Format object.
@@ -214,6 +215,38 @@ class File(h5py.File):
calendar_time_points=calendar_time_points,
default=True,
)
+ else:
+ # A quick validation to find h5py files which are not robofish.io files
+ if any([a not in self.attrs for a in ["world_size_cm", "format_version"]]):
+ msg = f"The opened file {self.path} does not include world_size_cm or format_version. It seems that the file is not a robofish.io.File."
+ if strict_validate:
+ raise KeyError(msg)
+ else:
+ warnings.warn(msg)
+ return
+
+ # Validate that the stored poses hash still fits.
+ if validate_poses_hash:
+ for entity in self.entities:
+ if "poses_hash" in entity.attrs:
+ if entity.attrs["poses_hash"] != entity.poses_hash:
+ warnings.warn(
+ f"The stored hash is not identical with the newly calculated hash. In entity {entity.name} in {self.path}. f.entity_actions_turns_speeds and f.entity_orientation_rad will return wrong results.\n"
+ f"stored: {entity.attrs['poses_hash']}, calculated: {entity.poses_hash}"
+ )
+ assert (
+ "unfinished_calculations" not in entity.attrs
+ ), f"The calculated data of file {self.path} is uncomplete and was probably aborted during calculation. please recalculate with `robofish-io-update-calculated-data {self.path}`."
+
+ else:
+ warnings.warn(
+ f"The file did not include pre-calculated data so the actions_speeds_turns "
+ f"and orientations_rad will have to be be recalculated everytime.\n"
+ f"Please use `robofish-io-update-calculated-data {self.path}` in the "
+ f"commandline or\nopen and close the file with robofish.io.File(f, 'r+') "
+ f"in python.\nIf the data should be recalculated every time open the file "
+ "with the bool option validate_poses_hash=False."
+ )
if validate:
self.validate(strict_validate)
@@ -225,8 +258,14 @@ class File(h5py.File):
if (type, value, traceback) == (None, None, None):
if self.mode != "r": # No need to validate read only files (performance).
self.validate()
+
super().__exit__(type, value, traceback)
+ def close(self):
+ if self.mode != "r":
+ self.update_calculated_data()
+ super().close()
+
def save_as(
self,
path: Union[str, Path],
@@ -243,6 +282,7 @@ class File(h5py.File):
The file itself, so something like f = robofish.io.File().save_as("file.hdf5") works
"""
+ self.update_calculated_data()
self.validate(strict_validate=strict_validate)
# Ensure all buffered data has been written to disk
@@ -471,6 +511,10 @@ class File(h5py.File):
)
return entity_names
+ def update_calculated_data(self, verbose=False):
+ for e in self.entities:
+ e.update_calculated_data(verbose)
+
def clear_calculated_data(self, verbose=True):
"""Delete all calculated data from the files."""
txt = ""
@@ -1129,7 +1173,7 @@ class File(h5py.File):
frames=n_frames,
init_func=init,
blit=platform.system() != "Darwin",
- interval=self.frequency,
+ interval=1000 / self.frequency,
repeat=False,
)
diff --git a/tests/resources/nan_test.hdf5 b/tests/resources/nan_test.hdf5
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diff --git a/tests/resources/valid_1.hdf5 b/tests/resources/valid_1.hdf5
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delta 198
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diff --git a/tests/resources/valid_2.hdf5 b/tests/resources/valid_2.hdf5
index 10caedaafa4d0d13c4be720f2c8d48dec184a092..eb8c69e1a01f1704c29c94b7c85590c5443275dd 100644
GIT binary patch
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diff --git a/tests/robofish/io/test_app_io.py b/tests/robofish/io/test_app_io.py
index ea4933f..6c3a16f 100644
--- a/tests/robofish/io/test_app_io.py
+++ b/tests/robofish/io/test_app_io.py
@@ -2,7 +2,6 @@ import robofish.io.app as app
from robofish.io import utils
import pytest
import logging
-from pathlib import Path
logging.getLogger().setLevel(logging.INFO)
@@ -19,11 +18,16 @@ def test_app_validate():
self.path = path
self.output_format = output_format
- raw_output = app.validate(DummyArgs([resources_path], "raw"))
+ # invalid.hdf5 should pass a warning
+ with pytest.warns(UserWarning):
+ raw_output = app.validate(DummyArgs([resources_path], "raw"))
# The three files valid.hdf5, almost_valid.hdf5, and invalid.hdf5 should be found.
assert len(raw_output) == 4
- app.validate(DummyArgs([resources_path], "human"))
+
+ # invalid.hdf5 should pass a warning
+ with pytest.warns(UserWarning):
+ app.validate(DummyArgs([resources_path], "human"))
def test_app_print():
--
GitLab