move to snake fmri naming.

README.md

@@ -17,23 +17,23 @@ simfmri comes with helper tools to configure and run simulation, and as such can
 ## Available commands 
 
 3 CLI interfaces are able to use the configuration folder to perform differents task: 
- - `simfmri-main` to do a full simulation + reconstruction + validation 
- - `simfmri-data` to generate a dataset of simulation
- - `simfmri-rec` to evaluate reconstructions methods (and do the statistics) over an existing dataset. 
+ - `snkf-main` to do a full simulation + reconstruction + validation 
+ - `snkf-data` to generate a dataset of simulation
+ - `snkf-rec` to evaluate reconstructions methods (and do the statistics) over an existing dataset. 
 
- Typically you would create a dataset with `simfmri-data` and then run `simfmri-rec` on it.
+ Typically you would create a dataset with `snkf-data` and then run `snkf-rec` on it.
 
 
 ## Configurations Files
-The configuration  are located in `simfmri/runner/conf` and articulates over 3 main componenents: 
+The configuration  are located in `snkf/runner/conf` and articulates over 3 main componenents: 
 - the simulation
 - the reconstruction
 - the validation via statistical analysis
 
 ### Simulation 
-located in `simfmri/runner/conf/simulation`
+located in `snkf/runner/conf/simulation`
 ### Reconstruction
-located in `simfmri/runner/conf/reconstruction`
+located in `snkf/runner/conf/reconstruction`
 
 ### Validation
 

docs/_toc.yml

@@ -19,11 +19,11 @@ parts:
   - caption: API References
     chapters:
       - file: api.rst
-      # - file: _api/simfmri.simulation.rst
-      # - file: _api/simfmri.handlers.rst
-      # - file: _api/simfmri.reconstructor.rst
-      # - file: _api/simfmri.cli.rst
-      # - file: _api/simfmri.analysis.rst
+      # - file: _api/snkf.simulation.rst
+      # - file: _api/snkf.handlers.rst
+      # - file: _api/snkf.reconstructor.rst
+      # - file: _api/snkf.cli.rst
+      # - file: _api/snkf.analysis.rst
 
   - caption: Extras
     chapters:

docs/advanced_guide/understanding_handlers.md

@@ -20,7 +20,7 @@ Handlers can be chained to create a complex simulation.
 ## Listing availables handlers
 
 ```{code-cell} ipython3
-from simfmri.handlers import H, list_handlers, HandlerChain
+from snkf.handlers import H, list_handlers, HandlerChain
 ```
 
 ```{code-cell} ipython3

docs/advanced_guide/writing_config_file.md

@@ -5,7 +5,7 @@
 ```
 
 <!-- #raw -->
-```{include} ../../../src/simfmri/conf/simulation/sl_basic.yaml
+```{include} ../../../src/snkf/conf/simulation/sl_basic.yaml
 ```
 <!-- #endraw -->
 

docs/api.rst

@@ -2,8 +2,8 @@
    :toctree: _autosummary
    :recursive:
 
-    simfmri.simulation
-    simfmri.handlers
-    simfmri.reconstructors
-    simfmri.cli
-    simfmri.analysis
+    snkf.simulation
+    snkf.handlers
+    snkf.reconstructors
+    snkf.cli
+    snkf.analysis

docs/build_docs.sh

@@ -3,7 +3,7 @@
 rm -rf _build _api
 
 # Build the API documentation with autoapi
-sphinx-apidoc -ePf --ext-autodoc --output-dir=_api -t _templates/ ../src/simfmri  "**/_version.py"
+sphinx-apidoc -ePf --ext-autodoc --output-dir=_api -t _templates/ ../src/snkf  "**/_version.py"
 
 # Finally build the entire docs
 jupyter-book build .

examples/README.rst

@@ -2,4 +2,4 @@
 Examples
 ========
 
-The following are a collection of examples showcasing the possibility of simfmri.
+The following are a collection of examples showcasing the possibility of snkf.

examples/example_big.py

@@ -7,7 +7,7 @@
 """
 
 import matplotlib.pyplot as plt
-from simfmri.utils.phantom import generate_phantom, raster_phantom
+from snkf.utils.phantom import generate_phantom, raster_phantom
 
 # %%
 # Rasterisation vs Generation

examples/example_shepp_logan.py

@@ -7,8 +7,8 @@
 
 import matplotlib.pyplot as plt
 
-from simfmri.simulation import SimData
-from simfmri.handlers import (
+from snkf.simulation import SimData
+from snkf.handlers import (
     SheppLoganGeneratorHandler,
     ActivationHandler,
     AcquisitionHandler,

examples/example_simulation_with_factory.py

@@ -23,24 +23,24 @@
 
 sim_config = """
 ### Simulation for a Shepp Logan phantom with activation.
-_target_: simfmri.simulation.SimDataFactory
+_target_: snkf.simulation.SimDataFactory
 checkpoints: false
 sim_params:
-  _target_: simfmri.simulation.SimulationParams
+  _target_: snkf.simulation.SimulationParams
   n_frames: 100
   shape: [128, 128, 128]
   sim_tr: 1.0
   n_coils: 1
 
 handlers:
   generator:
-    _target_: simfmri.simulation.SheppLoganGeneratorHandler
+    _target_: snkf.simulation.SheppLoganGeneratorHandler
   slicer:
-    _target_: simfmri.simulation.SlicerHandler
+    _target_: snkf.simulation.SlicerHandler
     axis: 0
     index: 58
   activation:
-    _target_: simfmri.simulation.ActivationHandler.from_block_design
+    _target_: snkf.simulation.ActivationHandler.from_block_design
     event_name: block_on
     block_on: 3
     block_off: 3
@@ -56,7 +56,7 @@
 #
 # .. tip::
 #     For more information on Hydra and its configuration be sure to check the sister
-#     package ``simfmri_runner``.
+#     package ``snkf_runner``.
 #
 
 # %%

examples/example_vds_simrec.py

@@ -6,8 +6,8 @@
 """
 import matplotlib.pyplot as plt
 import numpy as np
-from simfmri.simulation import H, SimData, list_handlers
-from simfmri.runner.reconstructor import (
+from snkf.simulation import H, SimData, list_handlers
+from snkf.runner.reconstructor import (
     ZeroFilledReconstructor,
     SequentialReconstructor,
     LowRankPlusSparseReconstructor,

pyproject.toml

@@ -1,5 +1,5 @@
 [project]
-name = "simfmri"  # Required
+name = "snake-fmri"  # Required
 # corresponds to the "Summary" metadata field:
 description = "A simulator and validator of fMRI reconstruction methods."
 # This field corresponds to the "Description" metadata field:
@@ -64,9 +64,9 @@ doc = ["jupyter-book", "sphinx-book-theme<1.0.0"]
 "Source" = "https://github.com/paquiteau/simfmri"
 
 [project.scripts]
-simfmri-main ="simfmri.cli.main:main_app"
-simfmri-data ="simfmrmi.cli.generate_dataset:generate_data"
-simfmri-rec="simfmri.cli.eval_recon:eval_recon"
+snkf-main ="snkf.cli.main:main_app"
+snkf-data ="simfmrmi.cli.generate_dataset:generate_data"
+snkf-rec="snkf.cli.eval_recon:eval_recon"
 
 
 [build-system]
@@ -80,7 +80,7 @@ where=["src"]
 
 
 [tool.setuptools_scm]
-write_to = "src/simfmri/_version.py"
+write_to = "src/snkf/_version.py"
 version_scheme = "python-simplified-semver"
 local_scheme="no-local-version"
 
@@ -97,7 +97,7 @@ profile="black"
 [tool.pytest.ini_options]
 minversion = "6.0"
 addopts = [
-    "--cov=simfmri",
+    "--cov=snkf",
     "--cov-report=term-missing",
     "--cov-report=xml"
 ]

src/conf/3d-cartesian.yaml

@@ -49,7 +49,7 @@ hydra:
       _target_: hydra_callbacks.MultiRunGatherer
       aggregator:
         _partial_: true
-        _target_: simfmri.cli.utils.aggregate_results
+        _target_: snkf.cli.utils.aggregate_results
 
     latest_run:
       _target_: hydra_callbacks.LatestRunLink

src/conf/3d-sos.yaml

@@ -55,7 +55,7 @@ hydra:
       _target_: hydra_callbacks.MultiRunGatherer
       aggregator:
         _partial_: true
-        _target_: simfmri.cli.utils.aggregate_results
+        _target_: snkf.cli.utils.aggregate_results
 
     latest_run:
       _target_: hydra_callbacks.LatestRunLink

src/conf/__init__.py

@@ -1 +1 @@
-"""Hydra configuration files for simfmri."""
+"""Hydra configuration files for snkf."""

src/conf/config.yaml

@@ -28,7 +28,7 @@ hydra:
       _target_: hydra_callbacks.MultiRunGatherer
       aggregator:
         _partial_: true
-        _target_: simfmri.cli.utils.aggregate_results
+        _target_: snkf.cli.utils.aggregate_results
 
     latest_run:
       _target_: hydra_callbacks.LatestRunLink

src/conf/dataset_config.yaml

@@ -13,5 +13,5 @@ hydra:
       _target_: hydra_callbacks.GitInfo
       clean: false
     retrieve_dataset:
-      _target_: simfmri.runner.generate_dataset.RetrieveDatasetCallback
+      _target_: snkf.runner.generate_dataset.RetrieveDatasetCallback
       dataset_dir: datasets

src/conf/eval_recon.yaml

@@ -22,4 +22,4 @@ hydra:
   sweeper:
     max_batch_size: 10
     samples_per_job: 1
-    dataset_path: "/home/pac/gits/nsp/simfmri_runner/datasets/dataset.csv"
+    dataset_path: "/home/pac/gits/nsp/snkf_runner/datasets/dataset.csv"

src/conf/experiments/extend_sweep.yaml

@@ -14,17 +14,17 @@ hydra:
       reconstruction: lowrank_sparse, sequential, zero_filled
 
   run:
-    dir: /volatile/pierre-antoine/simfmri/outputs/${hydra.job.name}/${now:%Y-%m-%d_%H-%M-%S}
+    dir: /volatile/pierre-antoine/snkf/outputs/${hydra.job.name}/${now:%Y-%m-%d_%H-%M-%S}
   sweep:
-    dir: /volatile/pierre-antoine/simfmri/multirun/extend-sweep/${now:%Y-%m-%d}/${now:%H-%M-%S}
+    dir: /volatile/pierre-antoine/snkf/multirun/extend-sweep/${now:%Y-%m-%d}/${now:%H-%M-%S}
     subdir: ${hydra.job.num}
 
   callbacks:
     gather_files:
       _target_: hydra_callbacks.MultiRunGatherer
       result_file: "results.json"
       aggregator:
-        _target_: simfmri.runner.utils.aggregate_results
+        _target_: snkf.runner.utils.aggregate_results
         _partial_: true
 
     latest_link:

src/conf/experiments/sequentials.yaml

@@ -21,6 +21,6 @@ hydra:
 
   callbacks:
     gather_files:
-      _target_: simfmri.runner.callback.MultiRunGatherer
+      _target_: snkf.runner.callback.MultiRunGatherer
     latest_link:
-      _target_: simfmri.runner.callback.LatestRunLink
+      _target_: snkf.runner.callback.LatestRunLink

src/conf/scenario1.yaml

@@ -1,4 +1,4 @@
-# This files contains the configuration to reproduce the scenario 1 of the Simfmri paper.
+# This files contains the configuration to reproduce the scenario 1 of the Snkf paper.
 
 force_sim: false
 cache_dir: ${oc.env:PWD}/cache
@@ -56,7 +56,7 @@ hydra:
       _target_: hydra_callbacks.MultiRunGatherer
       aggregator:
         _partial_: true
-        _target_: simfmri.cli.utils.aggregate_results
+        _target_: snkf.cli.utils.aggregate_results
 
     latest_run:
       _target_: hydra_callbacks.LatestRunLink

src/conf/scenario2.yaml

@@ -72,7 +72,7 @@ hydra:
       _target_: hydra_callbacks.MultiRunGatherer
       aggregator:
         _partial_: true
-        _target_: simfmri.cli.utils.aggregate_results
+        _target_: snkf.cli.utils.aggregate_results
 
     latest_run:
       _target_: hydra_callbacks.LatestRunLink

src/simfmri/analysis/plotting.py → src/snkf/analysis/plotting.py

@@ -9,7 +9,7 @@
     from matplotlib.artist import Artist
     from matplotlib.axes import Axes
     from matplotlib.figure import Figure
-    from simfmri.simulation import SimData
+    from snkf.simulation import SimData
 
 from matplotlib.lines import Line2D
 from matplotlib.offsetbox import (

src/simfmri/analysis/stats.py → src/snkf/analysis/stats.py

@@ -10,7 +10,7 @@
 from nilearn.glm.thresholding import fdr_threshold
 from scipy.stats import norm
 
-from simfmri.simulation import SimData
+from snkf.simulation import SimData
 
 logger = logging.getLogger(__name__)
 

src/simfmri/cli/main.py → src/snkf/cli/main.py

@@ -13,10 +13,10 @@
 from hydra_callbacks import PerfLogger
 from omegaconf import DictConfig, OmegaConf
 
-from simfmri.analysis.stats import contrast_zscore, get_scores
-from simfmri.handlers import HandlerChain
-from simfmri.reconstructors import get_reconstructor
-from simfmri.cli.utils import hash_config
+from snkf.analysis.stats import contrast_zscore, get_scores
+from snkf.handlers import HandlerChain
+from snkf.reconstructors import get_reconstructor
+from snkf.cli.utils import hash_config
 
 logger = logging.getLogger(__name__)
 

src/simfmri/cli/sweeper.py → src/snkf/cli/sweeper.py

@@ -1,4 +1,4 @@
-"""A dataset sweeper for simfmri_runner."""
+"""A dataset sweeper for snkf_runner."""
 import itertools
 import logging
 import os

src/simfmri/cli/utils.py → src/snkf/cli/utils.py

@@ -8,7 +8,7 @@
 import itertools
 import numpy as np
 from collections.abc import Sequence
-from simfmri.simulation import SimData
+from snkf.simulation import SimData
 import logging
 from joblib.hashing import hash as jb_hash
 from omegaconf import DictConfig, OmegaConf

src/simfmri/handlers/acquisition/base.py → src/snkf/handlers/acquisition/base.py

@@ -10,8 +10,8 @@
 import numpy as np
 from mrinufft.io import read_trajectory
 
-from simfmri.simulation import SimData
-from simfmri.utils import AnyShape, validate_rng
+from snkf.simulation import SimData
+from snkf.utils import AnyShape, validate_rng
 
 from ..base import AbstractHandler
 from ._coils import get_smaps

src/simfmri/handlers/acquisition/cartesian_sampling.py → src/snkf/handlers/acquisition/cartesian_sampling.py

@@ -5,7 +5,7 @@
 from enum import Enum
 
 from typing import Sequence, Any, Literal
-from simfmri.utils import RngType, validate_rng, AnyShape
+from snkf.utils import RngType, validate_rng, AnyShape
 
 SlicerType = list[slice | np.ndarray[Any, np.dtype[np.int64]] | int]
 

src/simfmri/handlers/acquisition/trajectory.py → src/snkf/handlers/acquisition/trajectory.py

@@ -4,7 +4,7 @@
 from typing import Literal, Mapping, Any
 from collections.abc import Generator
 import numpy as np
-from simfmri.utils.typing import RngType, AnyShape
+from snkf.utils.typing import RngType, AnyShape
 
 from .cartesian_sampling import get_kspace_slice_loc
 

src/simfmri/handlers/acquisition/workers.py → src/snkf/handlers/acquisition/workers.py

@@ -18,7 +18,7 @@
 
 from tqdm.auto import tqdm
 
-from simfmri.simulation import SimData, LazySimArray
+from snkf.simulation import SimData, LazySimArray
 
 from ._tools import TrajectoryGeneratorType