Merge branch 'main' into preferential-graph

This commit is contained in:
moririn2528
2023-09-11 14:45:35 +09:00
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github: optuna
+21 -18
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@@ -1,11 +1,13 @@
Tutorial: Human-in-the-loop Optimization
========================================
.. _tutorial-hitl-objective-form-widgets:
Tutorial: Human-in-the-loop Optimization using Objective Form Widgets
=====================================================================
.. image:: ./images/hitl1.png
In tasks involving image generation, natural language, or speech synthesis, evaluating results mechanically can be tough, and human evaluation becomes crucial. Until now, managing such tasks with Optuna has been challenging. However, the introduction of Optuna Dashboard enables humans and optimization algorithms to work interactively and execute the optimization process.
In this tutorial, we will explain how to optimize hyperparameters to generate a simple image using Optuna Dashboard. While the tutorial focuses on a simple task, the same approach can be applied to for instance optimize more complex images, natural language, and speech.
In this tutorial, we will explain how to optimize hyperparameters to generate a simple image using Optuna Dashboard. While the tutorial focuses on a simple task, the same approach can be applied to for instance optimize more complex images, natural language, and speech.
The tutorial is organized as follows:
@@ -93,11 +95,11 @@ Given the above system, we carry out HITL optimization as follows:
Environment setup
^^^^^^^^^^^^^^^^^
To run `the script <https://github.com/optuna/optuna-dashboard/blob/main/examples/hitl/main.py>`_ used in this tutorial, you need to install two libraries:
To run `the script <https://github.com/optuna/optuna-dashboard/blob/main/examples/hitl/main.py>`_ used in this tutorial, you need to install following libraries:
.. code-block:: console
$ pip install "optuna>=3.2.0" "optuna-dashboard>=0.10.0" pillow
$ pip install "optuna>=3.3.0" "optuna-dashboard>=0.12.0" pillow
You will use SQLite for the storage backend in this tutorial. Ensure that the following library is installed:
@@ -179,7 +181,9 @@ Lets walk through the script we used for the optimization.
.. code-block:: python
:linenos:
def suggest_and_generate_image(study: optuna.Study, artifact_backend: FileSystemBackend) -> None:
def suggest_and_generate_image(
study: optuna.Study, artifact_store: FileSystemArtifactStore
) -> None:
# 1. Ask new parameters
trial = study.ask()
r = trial.suggest_int("r", 0, 255)
@@ -192,7 +196,7 @@ Lets walk through the script we used for the optimization.
image.save(image_path)
# 3. Upload Artifact
artifact_id = upload_artifact(artifact_backend, trial, image_path)
artifact_id = upload_artifact(trial, image_path, artifact_store)
artifact_path = get_artifact_path(trial, artifact_id)
# 4. Save Note
@@ -205,12 +209,12 @@ Lets walk through the script we used for the optimization.
)
save_note(trial, note)
In the ``suggest_and_generate_image`` function, a new Trial is obtained and new hyperparameters are suggested for that Trial. Based on those hyperparameters, an RGB image is generated as an artifact. The generated image is then uploaded to the Artifact Storage of the Optuna Dashboard, and the image is also displayed in the Dashboard's Note. For more information on how to use the Note feature, please refer to the API Reference of :func:`~optuna_dashboard.save_note`.
In the ``suggest_and_generate_image`` function, a new Trial is obtained and new hyperparameters are suggested for that Trial. Based on those hyperparameters, an RGB image is generated as an artifact. The generated image is then uploaded to the Artifact Store of the Optuna, and the image is also displayed in the Dashboard's Note. For more information on how to use the Note feature, please refer to the API Reference of :func:`~optuna_dashboard.save_note`.
.. code-block:: python
:linenos:
def start_optimization(artifact_backend: FileSystemBackend) -> NoReturn:
def start_optimization(artifact_store: FileSystemArtifactStore) -> NoReturn:
# 1. Create Study
study = optuna.create_study(
study_name="Human-in-the-loop Optimization",
@@ -218,10 +222,10 @@ In the ``suggest_and_generate_image`` function, a new Trial is obtained and new
sampler=optuna.samplers.TPESampler(constant_liar=True, n_startup_trials=5),
load_if_exists=True,
)
# 2. Set an objective name
study.set_metric_names(["Looks like sunset color?"])
# 3. Register ChoiceWidget
register_objective_form_widgets(
study,
@@ -234,15 +238,14 @@ In the ``suggest_and_generate_image`` function, a new Trial is obtained and new
],
)
# 4. Start Optimization
# 4. Start Human-in-the-loop Optimization
n_batch = 4
while True:
running_trials = study.get_trials(deepcopy=False, states=(TrialState.RUNNING,))
if len(running_trials) >= n_batch:
time.sleep(1) # Avoid busy-loop
continue
suggest_and_generate_image(study, artifact_backend)
suggest_and_generate_image(study, artifact_store)
The function ``start_optimization`` defines our loop for HITL optimization to generate an image resembling a sunset color.
@@ -256,10 +259,10 @@ The function ``start_optimization`` defines our loop for HITL optimization to ge
def main() -> NoReturn:
tmp_path = os.path.join(os.path.dirname(__file__), "tmp")
# 1. Create Artifact Store
artifact_path = os.path.join(os.path.dirname(__file__), "artifact")
artifact_backend = FileSystemBackend(base_path=artifact_path)
artifact_store = FileSystemArtifactStore(artifact_path)
if not os.path.exists(artifact_path):
os.mkdir(artifact_path)
@@ -268,11 +271,11 @@ The function ``start_optimization`` defines our loop for HITL optimization to ge
os.mkdir(tmp_path)
# 2. Run optimize loop
start_optimization(artifact_backend)
start_optimization(artifact_store)
In the ``main`` function, at first, the locations of the Artifact Store is set.
* At #1, the :class:`~optuna_dashboard.FileSystemBackend` is created, which is one of the Artifact Storage options used in the Optuna Dashboard. Artifact Storage is used to store artifacts (data, files, etc.) generated during Optuna trials. For more information, please refer to the API Reference.
* At #1, the `FileSystemArtifactStore <https://optuna.readthedocs.io/en/stable/reference/generated/optuna.artifacts.FileSystemArtifactStore.html>`_ is created, which is one of the Artifact Store options used in the Optuna. Artifact Store is used to store artifacts (data, files, etc.) generated during Optuna trials. For more information, please refer to the API Reference.
* At #2, `start_optimization()` function, which is described above, is called.
After that, two folders are created, artifact and tmp, and then ``start_optimization`` function is called to start the HITL optimization using Optuna.
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@@ -5,3 +5,4 @@ Tutorials
:maxdepth: 1
hitl
preferential-optimization
@@ -0,0 +1,135 @@
Tutorial: Preferential Optimization
===================================
What is Preferential Optimization?
----------------------------------
Preferential optimization is the way to optimize hyperparameters based on human preferences,
specifically by determining which trial is better when given a pair to compare.
Compared to the `human-in-the-loop optimization utilizing objective form widgets <tutorial-hitl-objective-form-widgets>`_,
which relies on absolute evaluations, preferential optimization significantly reduces fluctuations in the evaluators' criteria,
ensuring more consistent results.
In this tutorial, we will interactively optimize RGB values between 0 and 255 to generate a color that resembles the "sunset hue", which is the same problem setting as `this tutorial <tutorial-hitl-objective-form-widgets>`_.
Hence, familiarizing yourself with the tutorial on objective form widgets beforehand might offer a smoother understanding.
How to Run Preferential Optimization
------------------------------------
In preferential optimization, we run two programs simultaneously: `generator.py`_ which executes parameter sampling or image generation,
and the Optuna Dashboard which provides a user interface for human evaluation.
.. figure:: ./images/preferential-optimization/system-architecture.png
:alt: System Architecture
:align: center
:width: 800px
To start, ensure you have the necessary packages installed. You can do this by running the following command in your terminal:
.. code-block:: console
$ pip install "optuna>=3.3.0" "optuna-dashboard>=0.13.0b1" pillow botorch
Run a Python script below which you copied from `generator.py`_.
.. code-block:: console
$ python generator.py
Then run a following command to launch Optuna Dashboard in a separate process.
.. code-block:: console
$ optuna-dashboard sqlite:///example.db --artifact-dir ./artifact
In the command, the storage is set to ``sqlite:///example.db`` to persist Optuna's trial history.
To store the artifacts (output images), ``--artifact-dir ./artifact`` is specified.
.. code-block:: console
Listening on http://127.0.0.1:8080/
Hit Ctrl-C to quit.
When you run the command, you will see a message like the one above.
Please open `http://127.0.0.1:8080/dashboard/ <http://127.0.0.1:8080/dashboard/>`_ in your browser, then you can see the Optuna Dashboard as follows:
.. figure:: ./images/preferential-optimization/anim.gif
:alt: GIF animation for preferential optimization
:align: center
:width: 800px
Selecting the least sunset-like color from four trials to report human preferences.
Script Explanation
------------------
Here, we specify the SQLite database URL and setup the artifact store, a filesystem to store images generated during the trial.
.. code-block:: python
:linenos:
STORAGE_URL = "sqlite:///example.db"
artifact_path = os.path.join(os.path.dirname(__file__), "artifact")
artifact_store = FileSystemArtifactStore(base_path=artifact_path)
os.makedirs(artifact_path, exist_ok=True)
Within the ``main()`` function, we initialize the study with necessary parameters, including specifying the preferential sampler.
ote that the ``Study`` and ``Sampler`` instantiated here are different from the conventional Optuna's ``Study``` and the ``Sampler``.
Preferential optimization relies solely on the comparison results between trials, and there are no absolute evaluation values for each trial.
Therefore, it is necessary to create dedicated ``Study`` and ``Sampler`` objects.
.. code-block:: python
:linenos:
from optuna_dashboard.preferential import create_study
from optuna_dashboard.preferential.samplers.gp import PreferentialGPSampler
study = create_study(
n_generate=5,
study_name="Preferential Optimization",
storage=STORAGE_URL,
sampler=PreferentialGPSampler(),
load_if_exists=True,
)
Then, we create a loop that continuously checks if new trials should be generated, awaiting human evaluation if not.
Within the while loop, new trials are generated if the condition :meth:`~optuna_dashboard.preferential.PreferentialStudy.should_generate` returns ``True``.
For each trial, RGB values are sampled, and an image is generated with these values.
The image is saved temporarily, uploaded to artifact store, and then saved a Markdown note using :func:`~optuna_dashboard.save_note`.
.. code-block:: python
:linenos:
while True:
# If study.should_generate() returns False, the generator waits for human evaluation.
if not study.should_generate():
time.sleep(0.1) # Avoid busy-loop
continue
trial = study.ask()
# Ask new parameters
r = trial.suggest_int("r", 0, 255)
g = trial.suggest_int("g", 0, 255)
b = trial.suggest_int("b", 0, 255)
# Generate an image
image_path = os.path.join(tmpdir, f"sample-{trial.number}.png")
image = Image.new("RGB", (320, 240), color=(r, g, b))
image.save(image_path)
# Upload to Artifact store
artifact_id = upload_artifact(trial, image_path, artifact_store)
trial.set_user_attr("artifact_id", artifact_id)
print("RGB:", (r, g, b))
# Save a Markdown note
note = textwrap.dedent(
f"""\
![generated-image]({get_artifact_path(trial, artifact_id)})
(R, G, B) = ({r}, {g}, {b})
"""
)
.. _generator.py: https://github.com/optuna/optuna-dashboard/blob/main/examples/preferential-optimization/generator.py
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@@ -4,17 +4,19 @@ import time
from typing import NoReturn
import optuna
from optuna.artifacts import FileSystemArtifactStore
from optuna.artifacts import upload_artifact
from optuna.trial import TrialState
from optuna_dashboard import ChoiceWidget
from optuna_dashboard import register_objective_form_widgets
from optuna_dashboard import save_note
from optuna_dashboard.artifact import get_artifact_path
from optuna_dashboard.artifact import upload_artifact
from optuna_dashboard.artifact.file_system import FileSystemBackend
from PIL import Image
def suggest_and_generate_image(study: optuna.Study, artifact_backend: FileSystemBackend) -> None:
def suggest_and_generate_image(
study: optuna.Study, artifact_store: FileSystemArtifactStore
) -> None:
# 1. Ask new parameters
trial = study.ask()
r = trial.suggest_int("r", 0, 255)
@@ -27,7 +29,7 @@ def suggest_and_generate_image(study: optuna.Study, artifact_backend: FileSystem
image.save(image_path)
# 3. Upload Artifact
artifact_id = upload_artifact(artifact_backend, trial, image_path)
artifact_id = upload_artifact(trial, image_path, artifact_store)
artifact_path = get_artifact_path(trial, artifact_id)
# 4. Save Note
@@ -41,7 +43,7 @@ def suggest_and_generate_image(study: optuna.Study, artifact_backend: FileSystem
save_note(trial, note)
def start_optimization(artifact_backend: FileSystemBackend) -> NoReturn:
def start_optimization(artifact_store: FileSystemArtifactStore) -> NoReturn:
# 1. Create Study
study = optuna.create_study(
study_name="Human-in-the-loop Optimization",
@@ -72,7 +74,7 @@ def start_optimization(artifact_backend: FileSystemBackend) -> NoReturn:
if len(running_trials) >= n_batch:
time.sleep(1) # Avoid busy-loop
continue
suggest_and_generate_image(study, artifact_backend)
suggest_and_generate_image(study, artifact_store)
def main() -> NoReturn:
@@ -80,7 +82,7 @@ def main() -> NoReturn:
# 1. Create Artifact Store
artifact_path = os.path.join(os.path.dirname(__file__), "artifact")
artifact_backend = FileSystemBackend(base_path=artifact_path)
artifact_store = FileSystemArtifactStore(artifact_path)
if not os.path.exists(artifact_path):
os.mkdir(artifact_path)
@@ -89,7 +91,7 @@ def main() -> NoReturn:
os.mkdir(tmp_path)
# 2. Run optimize loop
start_optimization(artifact_backend)
start_optimization(artifact_store)
if __name__ == "__main__":
@@ -6,10 +6,10 @@ import textwrap
import time
from typing import NoReturn
from optuna.artifacts import FileSystemArtifactStore
from optuna.artifacts import upload_artifact
from optuna_dashboard import save_note
from optuna_dashboard.artifact import get_artifact_path
from optuna_dashboard.artifact import upload_artifact
from optuna_dashboard.artifact.file_system import FileSystemBackend
from optuna_dashboard.preferential import create_study
from optuna_dashboard.preferential.samplers.gp import PreferentialGPSampler
from PIL import Image
@@ -17,7 +17,7 @@ from PIL import Image
STORAGE_URL = "sqlite:///example.db"
artifact_path = os.path.join(os.path.dirname(__file__), "artifact")
artifact_backend = FileSystemBackend(base_path=artifact_path)
artifact_store = FileSystemArtifactStore(base_path=artifact_path)
os.makedirs(artifact_path, exist_ok=True)
@@ -32,7 +32,7 @@ def main() -> NoReturn:
with tempfile.TemporaryDirectory() as tmpdir:
while True:
# If n_comparison "best" trials (that are not reported bad) exists,
# If study.should_generate() returns False,
# the generator waits for human evaluation.
if not study.should_generate():
time.sleep(0.1) # Avoid busy-loop
@@ -50,7 +50,7 @@ def main() -> NoReturn:
image.save(image_path)
# 3. Upload Artifact
artifact_id = upload_artifact(artifact_backend, trial, image_path)
artifact_id = upload_artifact(trial, image_path, artifact_store)
trial.set_user_attr("artifact_id", artifact_id)
print("RGB:", (r, g, b))
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@@ -1,155 +1,41 @@
from __future__ import annotations
import math
from math import erfc
from typing import Any
from typing import Callable
from botorch.acquisition.analytic import LogExpectedImprovement
from botorch.models.gpytorch import GPyTorchModel
from botorch.optim import optimize_acqf
import botorch.acquisition.analytic
import botorch.models.model
import botorch.optim
import botorch.posteriors.gpytorch
import gpytorch.constraints
import gpytorch.kernels
import gpytorch.likelihoods.gaussian_likelihood
from gpytorch.likelihoods.gaussian_likelihood import GaussianLikelihood
from gpytorch.likelihoods.gaussian_likelihood import Interval
from gpytorch.likelihoods.gaussian_likelihood import Prior
from gpytorch.models.exact_gp import ExactGP
import gpytorch.module
from linear_operator.operators import DiagLinearOperator
from linear_operator.operators import LinearOperator
from linear_operator.utils.errors import NotPSDError
import numpy as np
import optuna
from optuna import distributions
from optuna import Study
from optuna._transform import _SearchSpaceTransform
from optuna.distributions import BaseDistribution
from optuna.search_space import IntersectionSearchSpace
from optuna.trial import FrozenTrial
import pyro
import pyro.infer.autoguide
import pyro.infer.mcmc
from scipy.special import erfcinv
import optuna._transform
import torch
from torch import Tensor
from .._system_attrs import get_preferences
class _WeightedGaussianLikelihood(GaussianLikelihood):
def __init__(
self,
weights: torch.Tensor | None = None,
noise_prior: Prior | None = None,
noise_constraint: Interval | None = None,
batch_shape: torch.Size = torch.Size(),
**kwargs: Any,
) -> None:
super().__init__(
noise_prior=noise_prior,
noise_constraint=noise_constraint,
batch_shape=batch_shape,
**kwargs,
)
self.weights = weights
def _shaped_noise_covar(
self, base_shape: torch.Size, *params: Any, **kwargs: Any
) -> Tensor | LinearOperator:
assert self.weights is not None
assert base_shape[-1] == self.weights.shape[-1]
return DiagLinearOperator(1.0 / self.weights) * super()._shaped_noise_covar(
base_shape, *params, **kwargs
)
def _sample_y(
preferences: np.ndarray,
cov_X_X: np.ndarray,
obs_noise_var: float,
cycles: int,
initial_sample: np.ndarray,
rng: np.random.RandomState,
) -> np.ndarray:
# TODO: Refactor and write tests for this function.
N = cov_X_X.shape[0]
M = len(preferences)
cov_X_X = cov_X_X + np.eye(N) * 1e-6 # Add jitter
cov_X_X_chol = np.linalg.cholesky(cov_X_X)
cov_X_X_inv = np.linalg.inv(cov_X_X)
# (sI + A K A^T)^-1 = s^-1 I - s^-2 A(K^-1 + s^-1 A^T A)^-1 A^T
schur = cov_X_X_inv.copy()
np.add.at(schur, (preferences[:, 0], preferences[:, 0]), 1.0 / (2 * obs_noise_var))
np.add.at(schur, (preferences[:, 1], preferences[:, 1]), 1.0 / (2 * obs_noise_var))
np.add.at(schur, (preferences[:, 0], preferences[:, 1]), -1.0 / (2 * obs_noise_var))
np.add.at(schur, (preferences[:, 1], preferences[:, 0]), -1.0 / (2 * obs_noise_var))
idx_M = np.arange(M)
schur_inv = np.linalg.inv(schur)
cov_diff_inv = schur_inv[:, preferences[:, 0]] - schur_inv[:, preferences[:, 1]]
cov_diff_inv = cov_diff_inv[preferences[:, 0], :] - cov_diff_inv[preferences[:, 1], :]
cov_diff_inv *= -1 / (2 * obs_noise_var) ** 2
cov_diff_inv[idx_M, idx_M] += 1.0 / (2 * obs_noise_var)
diffs = _orthants_MVN_Gibbs_sampling(
cov_diff_inv,
cycles=cycles,
initial_sample=initial_sample[:, 0] - initial_sample[:, 1],
rng=rng,
)[-1]
random_ys = (cov_X_X_chol @ rng.randn(N))[preferences] + np.sqrt(obs_noise_var) * rng.randn(
M, 2
)
errors = diffs - (random_ys[:, 0] - random_ys[:, 1])
cov_diff_inv_errors = cov_diff_inv @ errors
AT_cov_diff_inv_errors = np.zeros((N,))
np.add.at(AT_cov_diff_inv_errors, preferences[:, 0], cov_diff_inv_errors)
np.add.at(AT_cov_diff_inv_errors, preferences[:, 1], -cov_diff_inv_errors)
return (
random_ys
+ (cov_X_X @ AT_cov_diff_inv_errors)[preferences]
+ obs_noise_var * np.array([[1, -1]]) * cov_diff_inv_errors[:, None]
)
_SQRT2 = math.sqrt(2)
def _orthants_MVN_Gibbs_sampling(
cov_inv: np.ndarray,
cycles: int,
initial_sample: np.ndarray,
rng: np.random.RandomState,
) -> np.ndarray:
def _orthants_MVN_Gibbs_sampling(cov_inv: Tensor, cycles: int, initial_sample: Tensor) -> Tensor:
dim = cov_inv.shape[0]
assert cov_inv.shape == (dim, dim)
if initial_sample is None:
sample_chain = np.zeros(dim)
else:
sample_chain = initial_sample
sample_chain = initial_sample
conditional_std = torch.rsqrt(torch.diag(cov_inv))
scaled_cov_inv = cov_inv / torch.diag(cov_inv)[:, None]
conditional_std = 1 / np.sqrt(np.diag(cov_inv))
scaled_cov_inv = cov_inv / np.c_[np.diag(cov_inv)]
out = np.empty((cycles + 1, dim))
out = torch.empty((cycles + 1, dim), dtype=torch.float64)
out[0, :] = sample_chain
for i in range(cycles):
for j in range(dim):
conditional_mean = sample_chain[j] - scaled_cov_inv[j] @ sample_chain
sample_chain[j] = (
_one_side_trunc_norm_sampling(
lower=-conditional_mean / conditional_std[j], rng=rng
)
_one_side_trunc_norm_sampling(lower=-conditional_mean / conditional_std[j])
* conditional_std[j]
+ conditional_mean
)
@@ -158,144 +44,234 @@ def _orthants_MVN_Gibbs_sampling(
return out
def _one_side_trunc_norm_sampling(lower: float, rng: np.random.RandomState) -> float:
return erfcinv(rng.rand() * erfc(lower / _SQRT2)) * _SQRT2
def _one_side_trunc_norm_sampling(lower: Tensor) -> Tensor:
if lower > 4.0:
r = torch.clamp_min(torch.rand(torch.Size(()), dtype=torch.float64), min=1e-300)
return (lower * lower - 2 * r.log()).sqrt()
else:
SQRT2 = math.sqrt(2)
r = torch.rand(torch.Size(()), dtype=torch.float64) * torch.erfc(lower / SQRT2)
while 1 - r == 1:
r = torch.rand(torch.Size(()), dtype=torch.float64) * torch.erfc(lower / SQRT2)
return torch.erfinv(1 - r) * SQRT2
class _PreferentialGP(GPyTorchModel, ExactGP):
_num_outputs = 1
_orthants_MVN_Gibbs_sampling_jit = torch.jit.script(_orthants_MVN_Gibbs_sampling)
def _compute_cov_diff_diff_inv(preferences: Tensor, cov_x_x: Tensor, noise_var: Tensor) -> Tensor:
N = cov_x_x.shape[0]
M = preferences.shape[0]
# (sI + A K A^T)^-1 = s^-1 I - s^-2 A(K^-1 + s^-1 A^T A)^-1 A^T
# (K^-1 + s^-1 A^T A)^-1 = K (I + s^-1 A^T A K)^-1 (To avoid computing K^-1)
I_plus_sinv_AT_A_K = torch.eye(N, dtype=torch.float64)
A_K = cov_x_x[preferences[:, 0], :] - cov_x_x[preferences[:, 1], :]
I_plus_sinv_AT_A_K.index_add_(0, preferences[:, 0], A_K * (1 / noise_var))
I_plus_sinv_AT_A_K.index_add_(0, preferences[:, 1], A_K * (-1 / noise_var))
schur_inv: Tensor = torch.linalg.solve(I_plus_sinv_AT_A_K, cov_x_x, left=False)
cov_diff_diff_inv = schur_inv[:, preferences[:, 0]] - schur_inv[:, preferences[:, 1]]
cov_diff_diff_inv = (
cov_diff_diff_inv[preferences[:, 0], :] - cov_diff_diff_inv[preferences[:, 1], :]
)
cov_diff_diff_inv *= -1 / noise_var**2
idx_M = torch.arange(M)
cov_diff_diff_inv[idx_M, idx_M] += 1.0 / noise_var
return cov_diff_diff_inv
class _SampledGP(botorch.models.model.Model):
def __init__(
self,
kernel: gpytorch.kernels.Kernel,
noise_prior: Prior | None = None,
noise_constraint: Interval | None = None,
kernel_func: Callable[[Tensor, Tensor], Tensor],
x: Tensor,
preferences: Tensor,
noise_var: Tensor,
diff: Tensor,
) -> None:
GPyTorchModel.__init__(self)
likelihood = _WeightedGaussianLikelihood(
noise_prior=noise_prior, noise_constraint=noise_constraint
super().__init__()
self.kernel_func = kernel_func
self.x = x
self.preferences = preferences
self.diff = diff
self.noise_var = noise_var
self._cov_diff_diff_inv = _compute_cov_diff_diff_inv(
preferences=preferences,
cov_x_x=self.kernel_func(x, x),
noise_var=noise_var,
)
ExactGP.__init__(self, train_inputs=None, train_targets=None, likelihood=likelihood)
self.covar_module = kernel
self._last_params: dict[str, torch.Tensor] | None = None
self._last_mcmc_step_size: float | None = None
def posterior(
self,
X: Tensor,
output_indices: list[int] | None = None,
observation_noise: bool = False,
posterior_transform: Any | None = None,
**kwargs: Any,
) -> botorch.posteriors.gpytorch.GPyTorchPosterior:
assert posterior_transform is None
assert output_indices is None
assert self.x.shape[-1] == X.shape[-1]
def _pyro_model(self, train_x: torch.Tensor, train_y: torch.Tensor) -> None:
# with gpytorch.settings.fast_computations(False, False, False):
sampled_model = self.pyro_sample_from_prior()
x_expanded = self.x.expand(X.shape[:-2] + (self.x.shape[-2], X.shape[-1]))
ys = sampled_model.likelihood(sampled_model.forward(train_x))
cov_X_x = self.kernel_func(X, x_expanded)
cov_X_diff = cov_X_x[..., self.preferences[:, 0]] - cov_X_x[..., self.preferences[:, 1]]
pyro.sample("y", ys, obs=train_y)
mean = cov_X_diff @ (self._cov_diff_diff_inv @ self.diff)
cov = self.kernel_func(X, X) - cov_X_diff @ self._cov_diff_diff_inv @ cov_X_diff.transpose(
-1, -2
)
if observation_noise:
idx = torch.arange(cov.shape[-1])
cov[..., idx, idx] += self.noise_var
def fit_mcmc(
self, X: torch.Tensor, preferences: torch.Tensor, cycles: int, rng: np.random.RandomState
) -> None:
return botorch.posteriors.gpytorch.GPyTorchPosterior(
distribution=gpytorch.distributions.MultivariateNormal(
mean=mean,
covariance_matrix=cov,
)
)
@property
def batch_shape(self) -> torch.Size:
return torch.Size()
@property
def num_outputs(self) -> int:
return 1
def _truncnorm_mean_var_logz(alpha: Tensor) -> tuple[Tensor, Tensor, Tensor]:
SQRT_HALF = math.sqrt(0.5)
SQRT_HALF_PI = math.sqrt(0.5 * math.pi)
logz = torch.special.log_ndtr(-alpha)
mean = 1 / (SQRT_HALF_PI * torch.special.erfcx(alpha * SQRT_HALF))
var = 1 - mean * (mean - alpha)
return mean, var, logz
def _orthants_MVN_EP(
cov0: Tensor, preferences: Tensor, noise_var: Tensor, cycles: int
) -> tuple[Tensor, Tensor, Tensor]:
N = cov0.shape[0]
M = preferences.shape[0]
mu = torch.zeros(N, dtype=cov0.dtype)
cov = cov0.clone()
virtual_obs_a = [torch.tensor(0.0, dtype=cov0.dtype) for _ in range(M)]
virtual_obs_b = [torch.tensor(0.0, dtype=cov0.dtype) for _ in range(M)]
log_zs = torch.zeros(M, dtype=cov0.dtype)
for _ in range(cycles):
for i in range(M):
pref_i = preferences[i, :]
mean1 = mu[pref_i[0]] - mu[pref_i[1]]
Sxy = cov[pref_i[0]] - cov[pref_i[1]]
var1 = Sxy[pref_i[0]] - Sxy[pref_i[1]]
r0 = (1 - var1 * virtual_obs_a[i]).reciprocal()
var0 = var1 * r0
mean0 = (mean1 + var1 * virtual_obs_b[i]) * r0
obs_var = var0 + noise_var
obs_sigma = torch.sqrt(obs_var)
alpha = -mean0 / torch.clamp_min(obs_sigma, min=1e-20)
mean_norm, var_norm, logz = _truncnorm_mean_var_logz(alpha)
kalman_factor = var0 / torch.clamp_min(obs_var, min=1e-20)
mean2 = mean0 + obs_sigma * mean_norm * kalman_factor
var2 = kalman_factor * (noise_var + var_norm * var0)
var1_var2_inv = torch.clamp_min(var1 * var2, min=1e-20).reciprocal()
db = (mean1 * var2 - mean2 * var1) * var1_var2_inv
da = (var1 - var2) * var1_var2_inv
virtual_obs_b[i] = virtual_obs_b[i] + db
virtual_obs_a[i] = virtual_obs_a[i] + da
dr = (1 + var1 * da).reciprocal()
mu = mu - Sxy * ((db + mean1 * da) * dr)
cov = cov - (Sxy[:, None] * (da * dr)) @ Sxy[None, :]
log_zs[i] = logz
return mu, cov, torch.sum(log_zs)
_orthants_MVN_EP_jit = torch.jit.script(_orthants_MVN_EP)
class _PreferentialGP:
def __init__(self, kernel: gpytorch.kernels.Kernel, noise_prior: Prior, dims: int) -> None:
self.kernel = kernel
self.noise_prior = noise_prior
self.dims = dims
self.diff = torch.empty((0,), dtype=torch.float64, requires_grad=False)
self.log_noise = torch.nn.Parameter(
torch.tensor(0.0, dtype=torch.float64), requires_grad=True
)
def fit_params_EP(self, X: Tensor, preferences: Tensor) -> None:
if len(preferences) == 0:
# Skip actual MCMC computation
self.set_train_data(
inputs=torch.empty((0, X.shape[-1])),
targets=torch.empty((0,)),
strict=False,
)
self.likelihood.weights = torch.empty((0,))
else:
dtype = torch.float64
return
tolerance = 1e-3
max_iter = 100
cnt = torch.bincount(preferences.reshape(-1))
mask = cnt > 0
train_x = X[mask]
weights = cnt[mask]
optim = torch.optim.LBFGS([*self.kernel.parameters(), self.log_noise])
assert isinstance(self.likelihood, _WeightedGaussianLikelihood)
self.likelihood.weights = weights
last_params = [p.detach().clone() for p in optim.param_groups[0]["params"]]
for _ in range(max_iter):
preferences_np = preferences.detach().numpy()
def closure() -> Tensor:
optim.zero_grad()
noise = self.log_noise.exp()
cov0 = self.kernel.forward(X, X).to_dense()
_, _, logz = _orthants_MVN_EP_jit(cov0, preferences, noise, cycles=2)
all_ys_np = np.zeros((len(preferences), 2))
train_y = torch.zeros(
(
len(
train_x,
)
),
dtype=dtype,
loss = -logz - self.noise_prior.log_prob(noise)
for _, _, prior, param, _ in self.kernel.named_priors():
loss = loss - prior.log_prob(param(self.kernel)).sum()
loss.backward()
return loss
optim.step(closure)
# Check for convergence
params = optim.param_groups[0]["params"]
for p_old, p_new in zip(last_params, params):
if torch.max(torch.abs(p_old - p_new)) > tolerance:
break
else:
break
last_params = [p.detach().clone() for p in params]
def sample_gp(self, x: Tensor, preferences: Tensor) -> _SampledGP:
self.fit_params_EP(x, preferences)
with torch.no_grad():
cov_diff_diff_inv = _compute_cov_diff_diff_inv(
preferences=preferences,
cov_x_x=self.kernel(x, x).to_dense(),
noise_var=self.log_noise.exp(),
)
nuts = pyro.infer.mcmc.NUTS(
model=self._pyro_model,
init_strategy=pyro.infer.autoguide.init_to_sample,
step_size=self._last_mcmc_step_size or 1.0,
original_diff_size = len(self.diff)
self.diff.resize_(len(preferences))
self.diff[original_diff_size:] = 0.0
self.diff = _orthants_MVN_Gibbs_sampling_jit(
cov_inv=cov_diff_diff_inv,
initial_sample=self.diff,
cycles=20,
)[-1]
return _SampledGP(
kernel_func=lambda x1, x2: self.kernel(x1, x2).to_dense(),
x=x,
preferences=preferences,
noise_var=self.log_noise.exp(),
diff=self.diff,
)
warmup_steps = max(0, cycles - 2)
nuts.setup(warmup_steps=warmup_steps, train_x=train_x, train_y=train_y)
raw_params = self._last_params or nuts.initial_params
for i in range(cycles):
params = {
name: nuts.transforms[name].inv(value) for name, value in raw_params.items()
}
_set_params(self, params)
self.set_train_data(train_x, train_y, strict=False)
all_ys_np = _sample_y(
preferences=preferences_np,
cov_X_X=self.covar_module(train_x).detach().numpy(),
obs_noise_var=float(self.likelihood.noise_covar.noise),
cycles=10,
initial_sample=all_ys_np,
rng=rng,
)
ys_sum_np = np.zeros((len(X),))
np.add.at(ys_sum_np, preferences_np.reshape(-1), all_ys_np.reshape(-1))
ys_sum = torch.from_numpy(ys_sum_np)
train_y[:] = ys_sum[mask] / cnt[mask]
nuts.clear_cache()
try:
raw_params = nuts.sample(raw_params)
except NotPSDError:
nuts.cleanup()
nuts = pyro.infer.mcmc.NUTS(
model=self._pyro_model,
init_strategy=pyro.infer.autoguide.init_to_sample,
step_size=self._last_mcmc_step_size or 1.0,
)
nuts.setup(warmup_steps=warmup_steps, train_x=train_x, train_y=train_y)
raw_params = nuts.initial_params
params = {name: nuts.transforms[name].inv(value) for name, value in raw_params.items()}
self.set_train_data(train_x, train_y, strict=False)
_set_params(self, params)
self._last_params = raw_params
self._last_mcmc_step_size = nuts.step_size
nuts.cleanup()
def forward(self, x: torch.Tensor) -> gpytorch.distributions.MultivariateNormal:
mean_module = gpytorch.means.ZeroMean()
return gpytorch.distributions.MultivariateNormal(
mean_module(x),
self.covar_module(x),
)
def _set_params(
module: gpytorch.Module,
params_dict: dict[str, torch.Tensor],
memo: set | None = None,
prefix: str = "",
) -> None:
if memo is None:
memo = set()
if hasattr(module, "_priors"):
for name, (prior, closure, setting_closure) in module._priors.items():
if prior is not None and prior not in memo:
memo.add(prior)
setting_closure(module, params_dict[prefix + ("." if prefix else "") + name])
for mname, module_ in module.named_children():
submodule_prefix = prefix + ("." if prefix else "") + mname
_set_params(module_, params_dict, memo=memo, prefix=submodule_prefix)
class PreferentialGPSampler(optuna.samplers.BaseSampler):
@@ -306,18 +282,16 @@ class PreferentialGPSampler(optuna.samplers.BaseSampler):
noise_prior: Prior | None = None,
independent_sampler: optuna.samplers.BaseSampler | None = None,
seed: int | None = None,
device: torch.device | None = None,
) -> None:
self._rng = np.random.RandomState(seed)
self._search_space = IntersectionSearchSpace()
self.kernel = kernel
self.noise_prior = noise_prior
self.independent_sampler = independent_sampler or optuna.samplers.RandomSampler(
seed=self._rng.randint(2**32),
)
self.device = device or torch.device("cpu")
self.noise_prior = noise_prior or gpytorch.priors.GammaPrior(5.0, 50.0)
self._rng = np.random.RandomState(seed)
self.independent_sampler = independent_sampler or optuna.samplers.RandomSampler(
seed=self._rng.randint(2**32)
)
self._search_space = optuna.search_space.IntersectionSearchSpace()
self._gp: _PreferentialGP | None = None
def reseed_rng(self) -> None:
@@ -325,75 +299,64 @@ class PreferentialGPSampler(optuna.samplers.BaseSampler):
self._rng = np.random.RandomState()
def infer_relative_search_space(
self, study: Study, trial: FrozenTrial
) -> dict[str, BaseDistribution]:
self, study: optuna.Study, trial: optuna.trial.FrozenTrial
) -> dict[str, optuna.distributions.BaseDistribution]:
return self._search_space.calculate(study)
def sample_relative(
self,
study: Study,
trial: FrozenTrial,
search_space: dict[str, BaseDistribution],
study: optuna.Study,
trial: optuna.trial.FrozenTrial,
search_space: dict[str, optuna.distributions.BaseDistribution],
) -> dict[str, Any]:
preferences = get_preferences(study.system_attrs)
if len(preferences) == 0:
return {}
trials = study.get_trials(deepcopy=False)
trials_with_preference = list({t for (b, w) in preferences for t in (b, w)})
ids = {t: i for i, t in enumerate(trials_with_preference)}
trans = optuna._transform._SearchSpaceTransform(
search_space, transform_log=True, transform_step=True, transform_0_1=True
)
params = torch.tensor(
np.array([trans.transform(trials[t].params) for t in trials_with_preference]),
dtype=torch.float64,
)
pref_ids = torch.tensor([[ids[b], ids[w]] for b, w in preferences], dtype=torch.int32)
with torch.random.fork_rng():
torch.manual_seed(self._rng.randint(2**32))
pyro.set_rng_seed(self._rng.randint(2**32))
if len(search_space) == 0:
return {}
preferences = get_preferences(study.system_attrs)
trials = study.get_trials(deepcopy=False)
if len(preferences) == 0:
return {}
trans = _SearchSpaceTransform(
search_space, transform_log=True, transform_step=True, transform_0_1=True
)
dims = len(trans.bounds)
self._gp = self._gp or _PreferentialGP(
kernel=self.kernel
or gpytorch.kernels.MaternKernel(
nu=2.5,
ard_num_dims=dims,
lengthscale_prior=gpytorch.priors.GammaPrior(3.0, 6.0),
lengthscale_constraint=gpytorch.constraints.Positive(),
nu=1.5,
ard_num_dims=len(trans.bounds),
lengthscale_prior=gpytorch.priors.GammaPrior(5.0, 10.0),
lengthscale_constraint=gpytorch.constraints.GreaterThan(
0.0,
transform=torch.exp,
inv_transform=torch.log,
),
),
noise_prior=self.noise_prior or gpytorch.priors.GammaPrior(1.1, 2.0),
noise_constraint=gpytorch.constraints.Positive(),
noise_prior=self.noise_prior,
dims=len(trans.bounds),
)
if self._gp.dims != len(trans.bounds):
raise NotImplementedError(
"The search space has changed. "
"Dynamic search space is not supported in PreferentialGPSampler."
)
ids: dict[int, int] = {}
params: list[torch.Tensor] = []
pref_ids: list[tuple[int, int]] = []
for better, worse in preferences:
for t in (better, worse):
if t not in ids:
ids[t] = len(ids)
params.append(trans.transform(trials[t].params))
pref_ids.append((ids[better], ids[worse]))
dtype = torch.float64
params_torch = torch.tensor(np.array(params), dtype=dtype, device=self.device)
pref_ids_torch = torch.tensor(
np.array(pref_ids),
dtype=torch.int32,
device=self.device,
)
self._gp.fit_mcmc(params_torch, pref_ids_torch, cycles=10, rng=self._rng)
self._gp.eval()
scores = self._gp(params_torch).mean
best_f = torch.max(scores)
acqf = LogExpectedImprovement(
model=self._gp,
best_f=best_f,
sampled_gp = self._gp.sample_gp(params, pref_ids)
acqf = botorch.acquisition.analytic.LogExpectedImprovement(
model=sampled_gp,
best_f=torch.max(sampled_gp.posterior(params[:, None, :]).mean),
)
# TODO: Make it possible to apply it on categorical variables
candidates, _ = optimize_acqf(
candidates, _ = botorch.optim.optimize_acqf(
acq_function=acqf,
bounds=torch.from_numpy(trans.bounds.T),
q=1,
@@ -407,10 +370,10 @@ class PreferentialGPSampler(optuna.samplers.BaseSampler):
def sample_independent(
self,
study: Study,
trial: FrozenTrial,
study: optuna.Study,
trial: optuna.trial.FrozenTrial,
param_name: str,
param_distribution: distributions.BaseDistribution,
param_distribution: optuna.distributions.BaseDistribution,
) -> Any:
return self.independent_sampler.sample_independent(
study, trial, param_name, param_distribution
@@ -0,0 +1,41 @@
import React, { FC } from "react"
import {
ThreejsArtifactViewer,
isThreejsArtifact,
} from "./ThreejsArtifactViewer"
import InsertDriveFileIcon from "@mui/icons-material/InsertDriveFile"
import { CardMedia } from "@mui/material"
export const ArtifactCardMedia: FC<{
artifact: Artifact
urlPath: string
height: string
}> = ({ artifact, urlPath, height }) => {
if (isThreejsArtifact(artifact)) {
return (
<ThreejsArtifactViewer
src={urlPath}
width={"100%"}
height={height}
hasGizmo={false}
filetype={artifact.filename.split(".").pop()}
/>
)
} else if (artifact.mimetype.startsWith("audio")) {
return (
<audio controls>
<source src={urlPath} type={artifact.mimetype} />
</audio>
)
} else if (artifact.mimetype.startsWith("image")) {
return (
<CardMedia
component="img"
height={height}
image={urlPath}
alt={artifact.filename}
/>
)
}
return <InsertDriveFileIcon sx={{ fontSize: 80 }} />
}
@@ -1,10 +1,17 @@
import * as THREE from "three"
import React, { useEffect, useState } from "react"
import React, { useEffect, useState, ReactNode } from "react"
import { Canvas } from "@react-three/fiber"
import { GizmoHelper, GizmoViewport, OrbitControls } from "@react-three/drei"
import { STLLoader } from "three/examples/jsm/loaders/STLLoader"
import { Rhino3dmLoader } from "three/examples/jsm/loaders/3DMLoader"
import { PerspectiveCamera } from "three"
import { Modal, Box } from "@mui/material"
export const isThreejsArtifact = (artifact: Artifact): boolean => {
return (
artifact.filename.endsWith(".stl") || artifact.filename.endsWith(".3dm")
)
}
interface ThreejsArtifactViewerProps {
src: string
@@ -109,3 +116,48 @@ export const ThreejsArtifactViewer: React.FC<ThreejsArtifactViewerProps> = (
</Canvas>
)
}
export const useThreejsArtifactModal = (): [
(path: string, artifact: Artifact) => void,
() => ReactNode
] => {
const [open, setOpen] = useState(false)
const [target, setTarget] = useState<[string, Artifact | null]>(["", null])
const openModal = (artifactUrlPath: string, artifact: Artifact) => {
setTarget([artifactUrlPath, artifact])
setOpen(true)
}
const renderDeleteStudyDialog = () => {
return (
<Modal
open={open}
onClose={() => {
setOpen(false)
setTarget(["", null])
}}
>
<Box
sx={{
position: "absolute",
top: "50%",
left: "50%",
transform: "translate(-50%, -50%)",
bgcolor: "background.paper",
borderRadius: "15px",
}}
>
<ThreejsArtifactViewer
src={target[0]}
width={`${innerWidth * 0.8}px`}
height={`${innerHeight * 0.8}px`}
hasGizmo={true}
filetype={target[1]?.filename.split(".").pop()}
/>
</Box>
</Modal>
)
}
return [openModal, renderDeleteStudyDialog]
}
@@ -0,0 +1,233 @@
import React, {
ChangeEventHandler,
DragEventHandler,
FC,
MouseEventHandler,
useRef,
useState,
} from "react"
import {
Typography,
Box,
useTheme,
IconButton,
Card,
CardContent,
CardActionArea,
} from "@mui/material"
import UploadFileIcon from "@mui/icons-material/UploadFile"
import DownloadIcon from "@mui/icons-material/Download"
import DeleteIcon from "@mui/icons-material/Delete"
import FullscreenIcon from "@mui/icons-material/Fullscreen"
import { actionCreator } from "../action"
import { useDeleteArtifactDialog } from "./DeleteArtifactDialog"
import {
useThreejsArtifactModal,
isThreejsArtifact,
} from "./ThreejsArtifactViewer"
import { ArtifactCardMedia } from "./ArtifactCardMedia"
export const TrialArtifactCards: FC<{ trial: Trial }> = ({ trial }) => {
const theme = useTheme()
const [openDeleteArtifactDialog, renderDeleteArtifactDialog] =
useDeleteArtifactDialog()
const [openThreejsArtifactModal, renderThreejsArtifactModal] =
useThreejsArtifactModal()
const width = "200px"
const height = "150px"
return (
<>
<Typography
variant="h5"
sx={{ fontWeight: theme.typography.fontWeightBold }}
>
Artifacts
</Typography>
<Box sx={{ display: "flex", flexWrap: "wrap", p: theme.spacing(1, 0) }}>
{trial.artifacts.map((artifact) => {
const urlPath = `/artifacts/${trial.study_id}/${trial.trial_id}/${artifact.artifact_id}`
return (
<Card
key={artifact.artifact_id}
sx={{
marginBottom: theme.spacing(2),
width: width,
margin: theme.spacing(0, 1, 1, 0),
}}
>
<ArtifactCardMedia
artifact={artifact}
urlPath={urlPath}
height={height}
/>
<CardContent
sx={{
display: "flex",
flexDirection: "row",
padding: `${theme.spacing(1)} !important`,
}}
>
<Typography
sx={{
p: theme.spacing(0.5, 0),
flexGrow: 1,
wordWrap: "break-word",
maxWidth: `calc(100% - ${
isThreejsArtifact(artifact)
? theme.spacing(12)
: theme.spacing(8)
})`,
}}
>
{artifact.filename}
</Typography>
{isThreejsArtifact(artifact) ? (
<IconButton
aria-label="show artifact 3d model"
size="small"
color="inherit"
sx={{ margin: "auto 0" }}
onClick={() => {
openThreejsArtifactModal(urlPath, artifact)
}}
>
<FullscreenIcon />
</IconButton>
) : null}
<IconButton
aria-label="delete artifact"
size="small"
color="inherit"
sx={{ margin: "auto 0" }}
onClick={() => {
openDeleteArtifactDialog(
trial.study_id,
trial.trial_id,
artifact
)
}}
>
<DeleteIcon />
</IconButton>
<IconButton
aria-label="download artifact"
size="small"
color="inherit"
download={artifact.filename}
sx={{ margin: "auto 0" }}
href={urlPath}
>
<DownloadIcon />
</IconButton>
</CardContent>
</Card>
)
})}
<TrialArtifactUploader trial={trial} width={width} height={height} />
</Box>
{renderDeleteArtifactDialog()}
{renderThreejsArtifactModal()}
</>
)
}
const TrialArtifactUploader: FC<{
trial: Trial
width: string
height: string
}> = ({ trial, width, height }) => {
const theme = useTheme()
const action = actionCreator()
const [dragOver, setDragOver] = useState<boolean>(false)
if (trial.state !== "Running" && trial.state !== "Waiting") {
return null
}
const inputRef = useRef<HTMLInputElement>(null)
const handleClick: MouseEventHandler = () => {
if (!inputRef || !inputRef.current) {
return
}
inputRef.current.click()
}
const handleOnChange: ChangeEventHandler<HTMLInputElement> = (e) => {
const files = e.target.files
if (files === null) {
return
}
action.uploadArtifact(trial.study_id, trial.trial_id, files[0])
}
const handleDrop: DragEventHandler = (e) => {
e.stopPropagation()
e.preventDefault()
const files = e.dataTransfer.files
setDragOver(false)
for (let i = 0; i < files.length; i++) {
action.uploadArtifact(trial.study_id, trial.trial_id, files[i])
}
}
const handleDragOver: DragEventHandler = (e) => {
e.stopPropagation()
e.preventDefault()
e.dataTransfer.dropEffect = "copy"
setDragOver(true)
}
const handleDragLeave: DragEventHandler = (e) => {
e.stopPropagation()
e.preventDefault()
e.dataTransfer.dropEffect = "copy"
setDragOver(false)
}
return (
<Card
sx={{
marginBottom: theme.spacing(2),
width: width,
minHeight: height,
margin: theme.spacing(0, 1, 1, 0),
border: dragOver
? `3px dashed ${theme.palette.mode === "dark" ? "white" : "black"}`
: `1px solid ${theme.palette.divider}`,
}}
onDragOver={handleDragOver}
onDragLeave={handleDragLeave}
onDrop={handleDrop}
>
<CardActionArea
onClick={handleClick}
sx={{
height: "100%",
}}
>
<CardContent
sx={{
display: "flex",
height: "100%",
flexDirection: "column",
justifyContent: "center",
alignItems: "center",
}}
>
<UploadFileIcon
sx={{ fontSize: 80, marginBottom: theme.spacing(2) }}
/>
<input
type="file"
ref={inputRef}
onChange={handleOnChange}
style={{ display: "none" }}
/>
<Typography>Upload a New File</Typography>
<Typography
sx={{ textAlign: "center", color: theme.palette.grey.A400 }}
>
Drag your file here or click to browse.
</Typography>
</CardContent>
</CardActionArea>
</Card>
)
}
+3 -466
View File
@@ -1,13 +1,4 @@
import React, {
ChangeEventHandler,
DragEventHandler,
FC,
MouseEventHandler,
ReactNode,
useMemo,
useRef,
useState,
} from "react"
import React, { FC, ReactNode, useMemo } from "react"
import {
Typography,
Box,
@@ -16,11 +7,6 @@ import {
IconButton,
Menu,
MenuItem,
Card,
CardContent,
CardMedia,
CardActionArea,
Modal,
} from "@mui/material"
import Chip from "@mui/material/Chip"
import Divider from "@mui/material/Divider"
@@ -32,11 +18,6 @@ import ListSubheader from "@mui/material/ListSubheader"
import FilterListIcon from "@mui/icons-material/FilterList"
import CheckBoxOutlineBlankIcon from "@mui/icons-material/CheckBoxOutlineBlank"
import CheckBoxIcon from "@mui/icons-material/CheckBox"
import UploadFileIcon from "@mui/icons-material/UploadFile"
import DownloadIcon from "@mui/icons-material/Download"
import DeleteIcon from "@mui/icons-material/Delete"
import FullscreenIcon from "@mui/icons-material/Fullscreen"
import InsertDriveFileIcon from "@mui/icons-material/InsertDriveFile"
import StopCircleIcon from "@mui/icons-material/StopCircle"
import { TrialNote } from "./Note"
@@ -45,9 +26,8 @@ import ListItemIcon from "@mui/material/ListItemIcon"
import { useRecoilValue } from "recoil"
import { artifactIsAvailable } from "../state"
import { actionCreator } from "../action"
import { useDeleteArtifactDialog } from "./DeleteArtifactDialog"
import { TrialFormWidgets } from "./TrialFormWidgets"
import { ThreejsArtifactViewer } from "./ThreejsArtifactViewer"
import { TrialArtifactCards } from "./TrialArtifactCards"
const states: TrialState[] = [
"Complete",
@@ -319,454 +299,11 @@ export const TrialListDetail: FC<{
value !== null ? renderInfo(key, value) : null
)}
</Box>
{artifactEnabled && <TrialArtifact trial={trial} />}
{artifactEnabled && <TrialArtifactCards trial={trial} />}
</Box>
)
}
const TrialArtifact: FC<{ trial: Trial }> = ({ trial }) => {
const theme = useTheme()
const action = actionCreator()
const [openDeleteArtifactDialog, renderDeleteArtifactDialog] =
useDeleteArtifactDialog()
const [dragOver, setDragOver] = useState<boolean>(false)
const [open3dModelViewer, setOpen3dModelViewer] = useState<{
[key: string]: boolean
}>({})
const width = "200px"
const height = "150px"
const inputRef = useRef<HTMLInputElement>(null)
const handleClick: MouseEventHandler = () => {
if (!inputRef || !inputRef.current) {
return
}
inputRef.current.click()
}
const handleOnChange: ChangeEventHandler<HTMLInputElement> = (e) => {
const files = e.target.files
if (files === null) {
return
}
action.uploadArtifact(trial.study_id, trial.trial_id, files[0])
}
const handleDrop: DragEventHandler = (e) => {
e.stopPropagation()
e.preventDefault()
const files = e.dataTransfer.files
setDragOver(false)
for (let i = 0; i < files.length; i++) {
action.uploadArtifact(trial.study_id, trial.trial_id, files[i])
}
}
const handleDragOver: DragEventHandler = (e) => {
e.stopPropagation()
e.preventDefault()
e.dataTransfer.dropEffect = "copy"
setDragOver(true)
}
const handleDragLeave: DragEventHandler = (e) => {
e.stopPropagation()
e.preventDefault()
e.dataTransfer.dropEffect = "copy"
setDragOver(false)
}
return (
<>
<Typography
variant="h5"
sx={{ fontWeight: theme.typography.fontWeightBold }}
>
Artifacts
</Typography>
<Box sx={{ display: "flex", flexWrap: "wrap", p: theme.spacing(1, 0) }}>
{trial.artifacts.map((a) => {
if (a.mimetype.startsWith("image")) {
return (
<Card
key={a.artifact_id}
sx={{
marginBottom: theme.spacing(2),
width: width,
margin: theme.spacing(0, 1, 1, 0),
}}
>
<CardMedia
component="img"
height={height}
image={`/artifacts/${trial.study_id}/${trial.trial_id}/${a.artifact_id}`}
alt={a.filename}
/>
<CardContent
sx={{
display: "flex",
flexDirection: "row",
padding: `${theme.spacing(1)} !important`,
}}
>
<Typography
sx={{
p: theme.spacing(0.5, 0),
flexGrow: 1,
wordWrap: "break-word",
maxWidth: `calc(100% - ${theme.spacing(8)})`,
}}
>
{a.filename}
</Typography>
<IconButton
aria-label="delete artifact"
size="small"
color="inherit"
sx={{ margin: "auto 0" }}
onClick={() => {
openDeleteArtifactDialog(
trial.study_id,
trial.trial_id,
a
)
}}
>
<DeleteIcon />
</IconButton>
<IconButton
aria-label="download artifact"
size="small"
color="inherit"
download={a.filename}
sx={{ margin: "auto 0" }}
href={`/artifacts/${trial.study_id}/${trial.trial_id}/${a.artifact_id}`}
>
<DownloadIcon />
</IconButton>
</CardContent>
</Card>
)
} else if (
a.filename.endsWith(".stl") ||
a.filename.endsWith(".3dm")
) {
return (
<Card
key={a.artifact_id}
sx={{
marginBottom: theme.spacing(2),
display: "flex",
flexDirection: "column",
width: width,
minHeight: "100%",
margin: theme.spacing(0, 1, 1, 0),
}}
>
<Box
sx={{
flexGrow: 1,
display: "flex",
justifyContent: "center",
alignItems: "center",
}}
>
<ThreejsArtifactViewer
src={`/artifacts/${trial.study_id}/${trial.trial_id}/${a.artifact_id}`}
width={width}
height={height}
hasGizmo={false}
filetype={a.filename.split(".").pop()}
/>
</Box>
<CardContent
sx={{
display: "flex",
flexDirection: "row",
padding: `${theme.spacing(1)} !important`,
}}
>
<Typography
sx={{
p: theme.spacing(0.5, 0),
flexGrow: 1,
wordWrap: "break-word",
maxWidth: `calc(100% - ${theme.spacing(12)})`,
}}
>
{a.filename}
</Typography>
<IconButton
aria-label="show artifact 3d model"
size="small"
color="inherit"
sx={{ margin: "auto 0" }}
onClick={() => {
setOpen3dModelViewer(() => {
const obj = { ...open3dModelViewer }
obj[a.artifact_id] = true
return obj
})
}}
>
<FullscreenIcon />
</IconButton>
<Modal
open={
a.artifact_id in open3dModelViewer
? open3dModelViewer[a.artifact_id]
: false
}
onClose={() => {
setOpen3dModelViewer(() => {
const obj = { ...open3dModelViewer }
obj[a.artifact_id] = false
return obj
})
}}
>
<Box
sx={{
position: "absolute",
top: "50%",
left: "50%",
transform: "translate(-50%, -50%)",
bgcolor: "background.paper",
borderRadius: "15px",
}}
>
<ThreejsArtifactViewer
src={`/artifacts/${trial.study_id}/${trial.trial_id}/${a.artifact_id}`}
width={`${innerWidth * 0.8}px`}
height={`${innerHeight * 0.8}px`}
hasGizmo={true}
filetype={a.filename.split(".").pop()}
/>
</Box>
</Modal>
<IconButton
aria-label="delete artifact"
size="small"
color="inherit"
sx={{ margin: "auto 0" }}
onClick={() => {
openDeleteArtifactDialog(
trial.study_id,
trial.trial_id,
a
)
}}
>
<DeleteIcon />
</IconButton>
<IconButton
aria-label="download artifact"
size="small"
color="inherit"
sx={{ margin: "auto 0" }}
download={a.filename}
href={`/artifacts/${trial.study_id}/${trial.trial_id}/${a.artifact_id}`}
>
<DownloadIcon />
</IconButton>
</CardContent>
</Card>
)
} else if (a.mimetype.startsWith("audio")) {
return (
<Card
key={a.artifact_id}
sx={{
marginBottom: theme.spacing(2),
display: "flex",
flexDirection: "column",
width: width,
minHeight: "100%",
margin: theme.spacing(0, 1, 1, 0),
}}
>
<Box
sx={{
flexGrow: 1,
display: "flex",
justifyContent: "center",
alignItems: "center",
}}
>
<audio controls>
<source
src={`/artifacts/${trial.study_id}/${trial.trial_id}/${a.artifact_id}`}
type={a.mimetype}
/>
</audio>
</Box>
<CardContent
sx={{
display: "flex",
flexDirection: "row",
padding: `${theme.spacing(1)} !important`,
}}
>
<Typography
sx={{
p: theme.spacing(0.5, 0),
flexGrow: 1,
maxWidth: `calc(100% - ${theme.spacing(8)})`,
}}
>
{a.filename}
</Typography>
<IconButton
aria-label="delete artifact"
size="small"
color="inherit"
sx={{ margin: "auto 0" }}
onClick={() => {
openDeleteArtifactDialog(
trial.study_id,
trial.trial_id,
a
)
}}
>
<DeleteIcon />
</IconButton>
<IconButton
aria-label="download artifact"
size="small"
color="inherit"
sx={{ margin: "auto 0" }}
download={a.filename}
href={`/artifacts/${trial.study_id}/${trial.trial_id}/${a.artifact_id}`}
>
<DownloadIcon />
</IconButton>
</CardContent>
</Card>
)
} else {
return (
<Card
key={a.artifact_id}
sx={{
marginBottom: theme.spacing(2),
display: "flex",
flexDirection: "column",
width: width,
minHeight: "100%",
margin: theme.spacing(0, 1, 1, 0),
}}
>
<Box
sx={{
flexGrow: 1,
display: "flex",
justifyContent: "center",
alignItems: "center",
}}
>
<InsertDriveFileIcon sx={{ fontSize: 80 }} />
</Box>
<CardContent
sx={{
display: "flex",
flexDirection: "row",
padding: `${theme.spacing(1)} !important`,
}}
>
<Typography
sx={{
p: theme.spacing(0.5, 0),
flexGrow: 1,
maxWidth: `calc(100% - ${theme.spacing(8)})`,
}}
>
{a.filename}
</Typography>
<IconButton
aria-label="delete artifact"
size="small"
color="inherit"
sx={{ margin: "auto 0" }}
onClick={() => {
openDeleteArtifactDialog(
trial.study_id,
trial.trial_id,
a
)
}}
>
<DeleteIcon />
</IconButton>
<IconButton
aria-label="download artifact"
size="small"
color="inherit"
sx={{ margin: "auto 0" }}
download={a.filename}
href={`/artifacts/${trial.study_id}/${trial.trial_id}/${a.artifact_id}`}
>
<DownloadIcon />
</IconButton>
</CardContent>
</Card>
)
}
})}
{trial.state === "Running" || trial.state === "Waiting" ? (
<Card
sx={{
marginBottom: theme.spacing(2),
width: width,
minHeight: height,
margin: theme.spacing(0, 1, 1, 0),
border: dragOver
? `3px dashed ${
theme.palette.mode === "dark" ? "white" : "black"
}`
: `1px solid ${theme.palette.divider}`,
}}
onDragOver={handleDragOver}
onDragLeave={handleDragLeave}
onDrop={handleDrop}
>
<CardActionArea
onClick={handleClick}
sx={{
height: "100%",
}}
>
<CardContent
sx={{
display: "flex",
height: "100%",
flexDirection: "column",
justifyContent: "center",
alignItems: "center",
}}
>
<UploadFileIcon
sx={{ fontSize: 80, marginBottom: theme.spacing(2) }}
/>
<input
type="file"
ref={inputRef}
onChange={handleOnChange}
style={{ display: "none" }}
/>
<Typography>Upload a New File</Typography>
<Typography
sx={{ textAlign: "center", color: theme.palette.grey.A400 }}
>
Drag your file here or click to browse.
</Typography>
</CardContent>
</CardActionArea>
</Card>
) : null}
</Box>
{renderDeleteArtifactDialog()}
</>
)
}
const getTrialListLink = (
studyId: number,
exclude: TrialState[],