Updating docs structure

INFN-MRI · Jan 18, 2024 · dcf44d7 · dcf44d7
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Showing 8 changed files with 21 additions and 18 deletions.
diff --git a/.../api/generated/deepmr.io.read_rawdata.rst → ...core/generated/deepmr.io.read_rawdata.rst b/.../api/generated/deepmr.io.read_rawdata.rst → ...core/generated/deepmr.io.read_rawdata.rst
diff --git a/docs/source/api/io.md → docs/source/core/io.md b/docs/source/api/io.md → docs/source/core/io.md
diff --git a/docs/source/api/optim.md → docs/source/core/optim.md b/docs/source/api/optim.md → docs/source/core/optim.md
diff --git a/docs/source/api/prox.md → docs/source/core/prox.md b/docs/source/api/prox.md → docs/source/core/prox.md
diff --git a/docs/source/index.md b/docs/source/index.md
@@ -2,6 +2,7 @@
 ```{include} ../../_README.md
 ```
 
+<!---
 ```{toctree}
 :hidden:
 :caption: User Guide
@@ -10,7 +11,9 @@ user_guide/getting_started.md
 user_guide/overview.md
 
 ```
+-->
 
+<!---
 ```{toctree}
 :hidden:
 :maxdepth: 2
@@ -21,14 +24,13 @@ tutorials/01-warmup-mri-recon.ipynb
 tutorials/02-dl-mri-recon.ipynb
 
 ```
+-->
 
 ```{toctree}
 :hidden:
-:caption: API References
+:caption: Core Modules
 
-api/io.md
-api/optim.md
-api/prox.md
+core/io.md
 
 ```
 

diff --git a/src/deepmr/__init__.py b/src/deepmr/__init__.py
@@ -2,9 +2,9 @@
 from importlib.metadata import version
 __version__ = version("deepmr")
 
-from . import bloch
+# from . import bloch
 from . import io
-from . import optim
+# from . import optim
 # from . import prox
 
 from .testdata import testdata
diff --git a/src/deepmr/io/image/dicom.py b/src/deepmr/io/image/dicom.py
@@ -3,6 +3,7 @@
 __all__ = ["read_dicom"]
 
 import glob
+import math
 import multiprocessing
 import os
 from multiprocessing.dummy import Pool as ThreadPool
@@ -251,8 +252,8 @@ def _cast_to_complex_ge(dsets_in):
         do_recon = False
 
     if magnitude and phase and do_recon:
-        scale = 2 * np.pi / 4095
-        offset = -np.pi
+        scale = 2 * math.pi / 4095
+        offset = -math.pi
         img = np.stack(magnitude, axis=0).astype(np.float32) * np.exp(
             1j * (scale * np.stack(phase, axis=0) + offset).astype(np.float32)
         )
@@ -264,8 +265,8 @@ def _cast_to_complex_ge(dsets_in):
     if np.iscomplexobj(img):
         phase = np.angle(img)
         phase[..., 1::2, :, :] = (
-            (1e5 * (phase[..., 1::2, :, :] + 2 * np.pi)) % (2 * np.pi * 1e5)
-        ) / 1e5 - np.pi
+            (1e5 * (phase[..., 1::2, :, :] + 2 * math.pi)) % (2 * math.pi * 1e5)
+        ) / 1e5 - math.pi
         img = np.abs(img) * np.exp(1j * phase)
 
     # count number of instances
@@ -302,8 +303,8 @@ def _cast_to_complex_philips(dsets_in):
             phase.append(dset.pixel_array)
 
     if magnitude and phase:
-        scale = 2 * np.pi / 4095
-        offset = -np.pi
+        scale = 2 * math.pi / 4095
+        offset = -math.pi
         img = np.stack(magnitude, axis=0).astype(np.float32) * np.exp(
             1j * (scale * np.stack(phase, axis=0) + offset).astype(np.float32)
         )
@@ -342,8 +343,8 @@ def _cast_to_complex_siemens(dsets_in):
             phase.append(dset.pixel_array)
 
     if magnitude and phase:
-        scale = 2 * np.pi / 4095
-        offset = -np.pi
+        scale = 2 * math.pi / 4095
+        offset = -math.pi
         img = np.stack(magnitude, axis=0).astype(np.float32) * np.exp(
             1j * (scale * np.stack(phase, axis=0) + offset).astype(np.float32)
         )

diff --git a/src/deepmr/io/image/nifti.py b/src/deepmr/io/image/nifti.py
@@ -2,9 +2,9 @@
 
 __all__ = ["read_nifti"]
 
-# import copy
 import glob
 import json
+import math
 import os
 
 import numpy as np
@@ -102,8 +102,8 @@ def _nifti_read(file_path, json_dict):
 
         # cast to complex image
         if data_phase.size != 0:
-            scale = 2 * np.pi / 4095
-            offset = -np.pi
+            scale = 2 * math.pi / 4095
+            offset = -math.pi
             data = data * np.exp(1j * scale * data_phase + offset)
         if data_real.size != 0 and data_imag.size != 0:
             data = data_real + 1j * data_imag
@@ -118,7 +118,7 @@ def _nifti_read(file_path, json_dict):
      # fix fftshift along z
     if np.iscomplexobj(data) and json_dict['Manufacturer'] == 'GE':
         phase = np.angle(data)
-        phase[..., 1::2, :, :] = ((1e5 * (phase[..., 1::2, :, :] + 2 * np.pi)) % (2 * np.pi * 1e5)) / 1e5 - np.pi
+        phase[..., 1::2, :, :] = ((1e5 * (phase[..., 1::2, :, :] + 2 * math.pi)) % (2 * math.pi * 1e5)) / 1e5 - math.pi
         data = np.abs(data) * np.exp(1j * phase)
 
     return np.ascontiguousarray(data.transpose()), head, affine