Adding k-space IO test, Black reformatting

docs/source/conf.py

@@ -6,9 +6,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = u"deepmr"
-copyright = u"2023, Matteo Cencini"
-author = u"Matteo Cencini"
+project = "deepmr"
+copyright = "2023, Matteo Cencini"
+author = "Matteo Cencini"
 
 # -- General configuration ---------------------------------------------------
 
@@ -17,27 +17,30 @@
 # ones.
 extensions = [
     "myst_nb",
-#    "autoapi.extension",
-	"sphinx.ext.autodoc",
-	"sphinx.ext.autosummary",
+    #    "autoapi.extension",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
     "sphinx.ext.viewcode",
 ]
 
-autodoc_mock_imports = ["deepinv",
-						"h5py",
-						"ismrmrd",
-						"mat73",
-						"matplotlib",
-						"nibabel",
-						"numpy",
-						"numba",
-						"pydicom",
-						"pywt",
-						"ptwt",
-						"scipy",
-						"torch",
-						"tqdm"]
+autodoc_mock_imports = [
+    "dacite",
+    "deepinv",
+    "h5py",
+    "ismrmrd",
+    "mat73",
+    "matplotlib",
+    "nibabel",
+    "numpy",
+    "numba",
+    "pydicom",
+    "pywt",
+    "ptwt",
+    "scipy",
+    "torch",
+    "tqdm",
+]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -62,5 +65,4 @@
         "image_dark": "https://github.com/INFN-PREDATOR/deep-mr/blob/main/docs/source/figures/deepmr_logo_dark.png?raw=true",
         "scale": "10%",
     },
-
 }

setup.cfg

@@ -49,6 +49,7 @@ python_requires = >=3.9
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.9"
+	dacite
     deepinv
     h5py
     ismrmrd

src/deepmr/__init__.py

@@ -1,10 +1,12 @@
 # read version from installed package
 from importlib.metadata import version
+
 __version__ = version("deepmr")
 
 # from . import bloch
 from . import io
+
 # from . import optim
 # from . import prox
 
-from .testdata import testdata
+from .testdata import testdata

src/deepmr/bloch/blocks/__init__.py

@@ -3,10 +3,9 @@
 from . import prep as _prep
 from . import readout as _readout
 
-from .prep import * # noqa
-from .readout import * # noqa
+from .prep import *  # noqa
+from .readout import *  # noqa
 
 __all__ = []
 __all__.extend(_prep.__all__)
 __all__.extend(_readout.__all__)
-

src/deepmr/bloch/blocks/prep.py

@@ -4,10 +4,11 @@
 
 from .. import ops
 
+
 def InversionPrep(TI, T1, T2, weight, k, inv_props):
     """
     Adiabatic inversion operator.
-    
+
     Consists of a 180° pulse followed by a crusher gradient.
 
     Args:
@@ -39,12 +40,12 @@ def InversionPrep(TI, T1, T2, weight, k, inv_props):
         return ops.CompositeOperator(Sinv, Einv, Tinv, name="Inversion Propagator")
     else:
         return ops.Identity(name="Inversion Propagator")
-    
-    
+
+
 def T2Prep(Tprep, T1, T2, weight, k, prep_props):
     """
     T2 prep operator.
-    
+
     Consists of a 90°-180°--90° composite pulse followed by a crusher gradient.
 
     Args:
@@ -79,6 +80,8 @@ def T2Prep(Tprep, T1, T2, weight, k, prep_props):
         )
         Sprep = ops.Spoil(name="Prep Crusher")
 
-        return ops.CompositeOperator(Sprep, T90m, Eprep, T180, Eprep, T90p, name="Inversion Propagator")
+        return ops.CompositeOperator(
+            Sprep, T90m, Eprep, T180, Eprep, T90p, name="Inversion Propagator"
+        )
     else:
-        return ops.Identity(name="Inversion Propagator")
+        return ops.Identity(name="Inversion Propagator")

src/deepmr/bloch/blocks/readout.py

@@ -28,12 +28,24 @@ def ExcPulse(states, B1, rf_props):
 
     return ops.RFPulse(device, nlocs=nlocs, B1=B1, name="Excitation Pulse", **rf_props)
 
-def FSEStep(states, ESP, T1, T2, weight=None, k=None, chemshift=None, D=None, v=None, grad_props=None):
+
+def FSEStep(
+    states,
+    ESP,
+    T1,
+    T2,
+    weight=None,
+    k=None,
+    chemshift=None,
+    D=None,
+    v=None,
+    grad_props=None,
+):
     """
     (Unbalanced) SSFP propagator.
-    
+
     Consists of rfpulse (omitted) - free precession - spoiling gradient.
-    
+
     Args:
         states (tensor): EPG states matrix.
         ESP (float): Echo Spacing in ms.
@@ -51,20 +63,23 @@ def FSEStep(states, ESP, T1, T2, weight=None, k=None, chemshift=None, D=None, v=
         TETRop (epgtorch.Operator): Propagator until next TR.
 
     """
-    X, S = _free_precess(states, 0.5 * ESP, T1, T2, weight, k, chemshift, D, v, grad_props) 
-
+    X, S = _free_precess(
+        states, 0.5 * ESP, T1, T2, weight, k, chemshift, D, v, grad_props
+    )
+
     # build Xpre and Xpost
     Xpre = ops.CompositeOperator(S, X, name="FSEpre")
     Xpost = ops.CompositeOperator(X, S, name="FSEpost")
 
     return Xpre, Xpost
 
+
 def bSSFPStep(states, TE, TR, T1, T2, weight=None, k=None, chemshift=None):
     """
     (Balanced) SSFP propagator.
-    
+
     Consists of rfpulse (omitted) - free precession.
-    
+
     Args:
         states (tensor): EPG states matrix.
         TE (float): Echo Time in ms.
@@ -84,15 +99,30 @@ def bSSFPStep(states, TE, TR, T1, T2, weight=None, k=None, chemshift=None):
 
     """
     XTE, _ = _free_precess(states, TE, T1, T2, weight, k, chemshift, None, None, None)
-    XTETR, _ = _free_precess(states, TR-TE, T1, T2, weight, k, chemshift, None, None, None)
+    XTETR, _ = _free_precess(
+        states, TR - TE, T1, T2, weight, k, chemshift, None, None, None
+    )
     return XTE, XTETR
 
-def SSFPFidStep(states, TE, TR, T1, T2, weight=None, k=None, chemshift=None, D=None, v=None, grad_props=None):
+
+def SSFPFidStep(
+    states,
+    TE,
+    TR,
+    T1,
+    T2,
+    weight=None,
+    k=None,
+    chemshift=None,
+    D=None,
+    v=None,
+    grad_props=None,
+):
     """
     (Unbalanced) SSFP propagator.
-    
+
     Consists of rfpulse (omitted) - free precession - spoiling gradient.
-    
+
     Args:
         states (tensor): EPG states matrix.
         TE (float): Echo Time in ms.
@@ -112,15 +142,30 @@ def SSFPFidStep(states, TE, TR, T1, T2, weight=None, k=None, chemshift=None, D=N
 
     """
     XTE, _ = _free_precess(states, TE, T1, T2, weight, k, chemshift, D, v, grad_props)
-    XTETR, S = _free_precess(states, TR-TE, T1, T2, weight, k, chemshift, D, v, grad_props)
+    XTETR, S = _free_precess(
+        states, TR - TE, T1, T2, weight, k, chemshift, D, v, grad_props
+    )
     return XTE, ops.CompositeOperator(S, XTETR, name="SSFPFid TE-TR Propagator")
 
-def SSFPEchoStep(states, TE, TR, T1, T2, weight=None, k=None, chemshift=None, D=None, v=None, grad_props=None):
+
+def SSFPEchoStep(
+    states,
+    TE,
+    TR,
+    T1,
+    T2,
+    weight=None,
+    k=None,
+    chemshift=None,
+    D=None,
+    v=None,
+    grad_props=None,
+):
     """
     (Reverse) SSFP propagator.
-    
+
     Consists of rfpulse (omitted) - spoiling gradient - free precession.
-    
+
     Args:
         states (tensor): EPG states matrix.
         TE (float): Echo Time in ms.
@@ -140,7 +185,9 @@ def SSFPEchoStep(states, TE, TR, T1, T2, weight=None, k=None, chemshift=None, D=
 
     """
     XTE, _ = _free_precess(states, TE, T1, T2, weight, k, chemshift, D, v, grad_props)
-    XTETR, S = _free_precess(states, TR-TE, T1, T2, weight, k, chemshift, D, v, grad_props)
+    XTETR, S = _free_precess(
+        states, TR - TE, T1, T2, weight, k, chemshift, D, v, grad_props
+    )
     return ops.CompositeOperator(S, XTE, name="SSFPFid TE-TR Propagator"), XTETR
 
 
@@ -155,7 +202,7 @@ def _free_precess(states, t, T1, T2, weight, k, chemshift, D, v, grad_props):
         grad_props.pop("duration")
     else:
         tau = 0.0
-        
+
     # parse
     device = states["F"].device
     nstates = states["F"].shape[-4]
@@ -179,10 +226,8 @@ def _free_precess(states, t, T1, T2, weight, k, chemshift, D, v, grad_props):
                 name="Relaxation-MT",
             )
         else:
-            E = ops.Relaxation(
-                device, t, T1, T2, name="Relaxation"
-            )
-
+            E = ops.Relaxation(device, t, T1, T2, name="Relaxation")
+
         # setup washout
         if hasV and "moving" in states:
             W = ops.FlowWash(
@@ -194,15 +239,15 @@ def _free_precess(states, t, T1, T2, weight, k, chemshift, D, v, grad_props):
             )
         else:
             W = ops.Identity(name="Inflow+Washout")
-    
+
         # set up diffusion
         if hasD:
             D = ops.DiffusionDamping(
                 device, tau, D, nstates, name="Diffusion Damping", **grad_props
             )
         else:
             D = ops.Identity(name="Diffusion until TE")
-    
+
         # set up flow
         if hasV:
             J = ops.FlowDephasing(
@@ -215,7 +260,6 @@ def _free_precess(states, t, T1, T2, weight, k, chemshift, D, v, grad_props):
         D = ops.Identity(name="Diffusion Damping")
         J = ops.Identity(name="Flow Dephasing")
         W = ops.Identity(name="Inflow-Washout")
-
 
     # set up gradient spoiling
     S = ops.Shift(name="Gradient Spoiling")
@@ -224,7 +268,3 @@ def _free_precess(states, t, T1, T2, weight, k, chemshift, D, v, grad_props):
     X = ops.CompositeOperator(W, J, D, E, name="Free Precession")
 
     return X, S
-
-
-
-