update changes in examples.

.gitignore

@@ -1,7 +1,7 @@
 # general things to ignore
 *build/
 dist/
-docs/_autosummary
+**/_autosummary*
 docs/auto_examples/
 *.egg-info/
 *.egg
@@ -13,9 +13,11 @@ __pycache__/
 .tox
 .cache
 
+_version.py
 # hydra
 outputs/
 multirun/
 # personal stuff
 scripts/
 datasets/
+benchmark/

examples/example_shepp_logan.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from simfmri.simulator import SimulationData
+from simfmri.simulator import SimData
 from simfmri.simulator import (
     SheppLoganGeneratorHandler,
     ActivationHandler,
@@ -30,10 +30,10 @@
 snr = 100
 
 # %%
-# This data is used to createa the main SimulationData object, which gather
+# This data is used to createa the main SimData object, which gather
 # all the data related to this simulation
 
-sim_data = SimulationData(shape=shape, n_frames=n_frames, sim_tr=1, n_coils=1)
+sim_data = SimData(shape=shape, n_frames=n_frames, sim_tr=1, n_coils=1)
 
 print(sim_data)
 

examples/example_simulation_with_factory.py

@@ -23,7 +23,7 @@
 
 sim_config = """
 ### Simulation for a Shepp Logan phantom with activation.
-_target_: simfmri.simulator.SimulationDataFactory
+_target_: simfmri.simulator.SimDataFactory
 checkpoints: false
 sim_params:
   _target_: simfmri.simulator.SimulationParams

examples/example_vds_simrec.py

@@ -6,7 +6,7 @@
 """
 import matplotlib.pyplot as plt
 import numpy as np
-from simfmri.simulator import H, SimulationData, list_handlers
+from simfmri.simulator import H, SimData, list_handlers
 from simfmri.runner.reconstructor import (
     ZeroFilledReconstructor,
     SequentialReconstructor,
@@ -21,7 +21,7 @@
 # ``lazy=True`` means that the data will be generated on the fly when needed.
 # This is useful to avoid storing large data in memory.
 
-sim = SimulationData(
+sim = SimData(
     (64, 64), sim_tr=0.1, sim_time=300, fov=0.192, n_coils=4, rng=42, lazy=True
 )