diff --git a/examples/example_reconstructions/gold_balls.mat b/examples/example_reconstructions/gold_balls.mat index 2c5f191..5d38fbf 100644 Binary files a/examples/example_reconstructions/gold_balls.mat and b/examples/example_reconstructions/gold_balls.mat differ diff --git a/examples/example_reconstructions/gold_balls_half0.mat b/examples/example_reconstructions/gold_balls_half0.mat new file mode 100644 index 0000000..45156d5 Binary files /dev/null and b/examples/example_reconstructions/gold_balls_half0.mat differ diff --git a/examples/example_reconstructions/gold_balls_half1.mat b/examples/example_reconstructions/gold_balls_half1.mat new file mode 100644 index 0000000..19961cf Binary files /dev/null and b/examples/example_reconstructions/gold_balls_half1.mat differ diff --git a/examples/gold_ball_ptycho.py b/examples/gold_ball_ptycho.py index cca46d4..c34cfe7 100644 --- a/examples/gold_ball_ptycho.py +++ b/examples/gold_ball_ptycho.py @@ -11,21 +11,18 @@ dataset = cdtools.datasets.Ptycho2DDataset.from_cxi(filename) model = cdtools.models.FancyPtycho.from_dataset(dataset, n_modes=2) # Let's do this reconstruction on the GPU, shall we? -model.to(device='cuda') -dataset.get_as(device='cuda') +#model.to(device='cuda') +#dataset.get_as(device='cuda') -# Now, we run a short reconstruction from the dataset -for loss in model.Adam_optimize(10, dataset, batch_size=50, schedule=True): - # And we liveplot the updates to the model as they happen - print(model.report()) - model.inspect(dataset) +with model.save_on_exit('example_reconstructions/gold_balls.mat', dataset): + # Now, we run a short reconstruction from the dataset + for loss in model.Adam_optimize(10, dataset, batch_size=50): + # And we liveplot the updates to the model as they happen + print(model.report()) + model.inspect(dataset) -# This orthogonalizes the incoherent probe modes -model.tidy_probes() - -# And we save out the results as a .mat file -io.savemat('example_reconstructions/gold_balls.mat', - model.save_results(dataset)) + # This orthogonalizes the incoherent probe modes + model.tidy_probes() # Finally, we plot the results model.inspect(dataset) diff --git a/examples/gold_ball_split.py b/examples/gold_ball_split.py new file mode 100644 index 0000000..89ca24a --- /dev/null +++ b/examples/gold_ball_split.py @@ -0,0 +1,36 @@ +import cdtools +from matplotlib import pyplot as plt +from scipy import io + +# First, we load an example dataset from a .cxi file +filename = 'example_data/AuBalls_700ms_30nmStep_3_6SS_filter.cxi' +dataset = cdtools.datasets.Ptycho2DDataset.from_cxi(filename) + +datasets = dataset.split() + +for idx, dataset in enumerate(datasets): + + print(f'Working on half {idx}') + # Next, we create a ptychography model from the dataset + # Note that we explicitly ask for two incoherent probe modes + model = cdtools.models.FancyPtycho.from_dataset(dataset, n_modes=2) + + # Let's do this reconstruction on the GPU, shall we? + #model.to(device='cuda') + #dataset.get_as(device='cuda') + + with model.save_on_exit(f'example_reconstructions/gold_balls_half{idx}.mat', + dataset): + # Now, we run a short reconstruction from the dataset + for loss in model.Adam_optimize(10, dataset, batch_size=50): + # And we liveplot the updates to the model as they happen + print(model.report()) + model.inspect(dataset) + + # This orthogonalizes the incoherent probe modes + model.tidy_probes() + +# Finally, we plot the results +model.inspect(dataset) +model.compare(dataset) +plt.show() diff --git a/src/cdtools/datasets/ptycho_2d_dataset.py b/src/cdtools/datasets/ptycho_2d_dataset.py index 7825582..55d84d8 100644 --- a/src/cdtools/datasets/ptycho_2d_dataset.py +++ b/src/cdtools/datasets/ptycho_2d_dataset.py @@ -4,8 +4,10 @@ from copy import copy import h5py import pathlib from cdtools.datasets import CDataset +from cdtools.datasets.random_selection import random_selection from cdtools.tools import data as cdtdata from cdtools.tools import plotting +from copy import deepcopy __all__ = ['Ptycho2DDataset'] @@ -253,3 +255,32 @@ class Ptycho2DDataset(CDataset): return plotting.plot_nanomap_with_images(self.translations.detach().cpu(), get_images, values=nanomap_values, nanomap_units=units, image_title='Diffraction Pattern', image_colorbar_title=cbar_title) + + def split(self): + """Splits a dataset into two pseudorandomly selected sub-datasets + """ + + # the selection is only 5,000 items long, so we repeat it to be long + # enough for the dataset + repeated_random_selection = (random_selection + * int(np.ceil(len(self) / len(random_selection)))) + + repeated_random_selection = np.array(repeated_random_selection) + # Here, I use a fixed random selection for reproducibility + cut_random_selection =repeated_random_selection.astype(bool)[:len(self)] + + dataset_1 = deepcopy(self) + dataset_1.translations = self.translations[cut_random_selection] + dataset_1.patterns = self.patterns[cut_random_selection] + if hasattr(self, 'intensities') and self.intensities is not None: + dataset_1.intensities = self.intensities[cut_random_selection] + + dataset_2 = deepcopy(self) + dataset_2.translations = self.translations[~cut_random_selection] + dataset_2.patterns = self.patterns[~cut_random_selection] + if hasattr(self, 'intensities') and self.intensities is not None: + dataset_2.intensities = self.intensities[~cut_random_selection] + + return dataset_1, dataset_2 + + diff --git a/src/cdtools/datasets/random_selection.py b/src/cdtools/datasets/random_selection.py new file mode 100644 index 0000000..0943de2 --- /dev/null +++ b/src/cdtools/datasets/random_selection.py @@ -0,0 +1 @@ +random_selection = [0, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 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scipy import io +from contextlib import contextmanager from .complex_lbfgs import MyLBFGS __all__ = ['CDIModel'] @@ -169,7 +171,50 @@ class CDIModel(t.nn.Module): results : dict A dictionary containing all the parameters and buffers of the model, i.e. the result of self.state_dict(), converted to numpy. """ - return {k: v.cpu().numpy() for k, v in self.state_dict().items()} + state_dict = {k: v.cpu().numpy() for k, v in self.state_dict().items()} + return { + 'state_dict': state_dict, + 'loss_train': np.array(self.loss_train), + } + + + def save_to_mat(self, filename, *args): + """Saves the results to a .mat file + + Parameters + ---------- + filename : str + The filename to save under + *args + Accepts any additional args that model.save_results needs, for this model + """ + return io.savemat(filename, self.save_results(*args)) + + @contextmanager + def save_on_exit(self, filename, *args, exception_filename=None): + """Saves the results of the model when the context is exited + + If you wrap the main body of your code in this context manager, + it will either save the results to a .mat file upon completion, + or when any exception is raised during execution. + + Parameters + ---------- + filename : str + The filename to save under, upon completion + *args + Accepts any additional args that model.save_results needs, for this model + exception_filename : str + Optional, a separate filename to use if an exception is raised during execution. Default is equal to filename + """ + try: + yield + self.save_to_mat(filename, *args) + except Exception as e: + if exception_filename is None: + exception_filename = filename + self.save_to_mat(exception_filename, *args) + raise e def AD_optimize(self, iterations, data_loader, optimizer,\ diff --git a/src/cdtools/models/bragg_2d_ptycho.py b/src/cdtools/models/bragg_2d_ptycho.py index 0cc6960..b0d4697 100644 --- a/src/cdtools/models/bragg_2d_ptycho.py +++ b/src/cdtools/models/bragg_2d_ptycho.py @@ -564,17 +564,33 @@ class Bragg2DPtycho(CDIModel): def save_results(self, dataset): + # This will save out everything needed to recreate the object + # in the same state, but it's not the best formatted. For example, + # "background" stores the square root of the background, etc. + base_results = super().save_results() + + # We also save out the main results in a more readable format basis = self.probe_basis.detach().cpu().numpy() - translations = self.corrected_translations(dataset).detach().cpu().numpy() + translations=self.corrected_translations(dataset).detach().cpu().numpy() + original_translations = dataset.translations.detach().cpu().numpy() probe = self.probe.detach().cpu().numpy() probe = probe * self.probe_norm.detach().cpu().numpy() obj = self.obj.detach().cpu().numpy() background = self.background.detach().cpu().numpy()**2 weights = self.weights.detach().cpu().numpy() - losses = np.array(self.loss_train) - - return {'basis':basis, 'translation':translations, - 'probe':probe,'obj':obj, - 'background':background, - 'weights':weights, - 'losses':losses} + oversampling = self.oversampling + wavelength = self.wavelength.cpu().numpy() + + results = { + 'basis': basis, + 'translations': translations, + 'original_translations': original_translations, + 'probe': probe, + 'obj': obj, + 'background': background, + 'oversampling': oversampling, + 'weights': weights, + 'wavelength': wavelength, + } + + return {**base_results, **results} diff --git a/src/cdtools/models/fancy_ptycho.py b/src/cdtools/models/fancy_ptycho.py index 5355a77..6b481d2 100644 --- a/src/cdtools/models/fancy_ptycho.py +++ b/src/cdtools/models/fancy_ptycho.py @@ -724,9 +724,9 @@ class FancyPtycho(CDIModel): # This will save out everything needed to recreate the object # in the same state, but it's not the best formatted. For example, # "background" stores the square root of the background, etc. - state_dict = super().save_results() + base_results = super().save_results() - # So, we also save out the main results in a more readable format + # We also save out the main results in a more readable format basis = self.probe_basis.detach().cpu().numpy() translations=self.corrected_translations(dataset).detach().cpu().numpy() original_translations = dataset.translations.detach().cpu().numpy() @@ -738,7 +738,7 @@ class FancyPtycho(CDIModel): oversampling = self.oversampling wavelength = self.wavelength.cpu().numpy() - return { + results = { 'basis': basis, 'translations': translations, 'original_translations': original_translations, @@ -748,6 +748,6 @@ class FancyPtycho(CDIModel): 'oversampling': oversampling, 'weights': weights, 'wavelength': wavelength, - 'state_dict': state_dict, } - + + return {**base_results, **results}