renaming package for pypi conflict

.gitignore

@@ -22,4 +22,4 @@ tmp/
 docs/generated/
 docs_build/
 
-src/mrsim/_version.py
+src/torchsim/_version.py

README.rst

@@ -1,30 +1,30 @@
-MRSim
-=====
+TorchSim
+========
 
-MRSim is a pure Pytorch-based MR simulator, including analytical and EPG model.
+TorchSim is a pure Pytorch-based MR simulator, including analytical and EPG model.
 
 |Coverage| |CI| |CD| |License| |Codefactor| |Sphinx| |PyPi| |Black| |PythonVersion|
 
-.. |Coverage| image:: https://infn-mri.github.io/mrsim/_static/coverage_badge.svg
-   :target: https://infn-mri.github.io/mrsim
+.. |Coverage| image:: https://infn-mri.github.io/torchsim/_static/coverage_badge.svg
+   :target: https://infn-mri.github.io/torchsim
 
-.. |CI| image:: https://github.com/INFN-MRI/mrsim/workflows/CI/badge.svg
-   :target: https://github.com/INFN-MRI/mrsim
+.. |CI| image:: https://github.com/INFN-MRI/torchsim/workflows/CI/badge.svg
+   :target: https://github.com/INFN-MRI/torchsim
 
-.. |CD| image:: https://github.com/INFN-MRI/mrsim/workflows/CD/badge.svg
-   :target: https://github.com/INFN-MRI/mrsim
+.. |CD| image:: https://github.com/INFN-MRI/torchsim/workflows/CD/badge.svg
+   :target: https://github.com/INFN-MRI/torchsim
 
-.. |License| image:: https://img.shields.io/github/license/INFN-MRI/mrsim
-   :target: https://github.com/INFN-MRI/mrsim/blob/main/LICENSE.txt
+.. |License| image:: https://img.shields.io/github/license/INFN-MRI/torchsim
+   :target: https://github.com/INFN-MRI/torchsim/blob/main/LICENSE.txt
 
-.. |Codefactor| image:: https://www.codefactor.io/repository/github/INFN-MRI/mrsim/badge
-   :target: https://www.codefactor.io/repository/github/INFN-MRI/mrsim
+.. |Codefactor| image:: https://www.codefactor.io/repository/github/INFN-MRI/torchsim/badge
+   :target: https://www.codefactor.io/repository/github/INFN-MRI/torchsim
 
 .. |Sphinx| image:: https://img.shields.io/badge/docs-Sphinx-blue
-   :target: https://infn-mri.github.io/mrsim
+   :target: https://infn-mri.github.io/torchsim
 
-.. |PyPi| image:: https://img.shields.io/pypi/v/mrsim
-   :target: https://pypi.org/project/mrsim
+.. |PyPi| image:: https://img.shields.io/pypi/v/torchsim
+   :target: https://pypi.org/project/torchsim
 
 .. |Black| image:: https://img.shields.io/badge/style-black-black
 
@@ -33,7 +33,7 @@ MRSim is a pure Pytorch-based MR simulator, including analytical and EPG model.
 
 Features
 --------
-MRSim contains tools to implement parallelized and differentiable MR simulators. Specifically, we provide
+TorchSim contains tools to implement parallelized and differentiable MR simulators. Specifically, we provide
 
 1. Automatic vectorization of across multiple atoms (e.g., voxels).
 2. Automatic generation of forward and jacobian methods (based on forward-mode autodiff) to be used in parameter fitting or model-based reconstructions.
@@ -44,24 +44,39 @@ MRSim contains tools to implement parallelized and differentiable MR simulators.
 Installation
 ------------
 
-MRSim can be installed via pip as:
+TorchSim can be installed via pip as:
 
 .. code-block:: bash
 
-    pip install mrsim
+    pip install torchsim
 
 Basic Usage
 -----------
+Using TorchSim, we can quickly implement and run MR simulations.
+We also provide pre-defined simulators for several applications:
+
+.. code-block:: python
+    
+    import numpy as np
+    import torchsim
+    
+    # generate a flip angle pattern
+    flip = np.concatenate((np.linspace(5, 60.0, 300), np.linspace(60.0, 2.0, 300), np.ones(280)*2.0))
+    sig, jac = torchsim.mrf_sim(flip=flip, TR=10.0, T1=1000.0, T2=100.0, diff=("T1","T2"))
+    
+This way we obtained the forward pass signal (``sig``) as well as the jacobian
+calculated with respect to ``T1`` and ``T2``.
+
 
 Development
-~~~~~~~~~~~
+-----------
 
-If you are interested in improving this project, install MRSim in editable mode:
+If you are interested in improving this project, install TorchSim in editable mode:
 
 .. code-block:: bash
 
-    git clone [email protected]:INFN-MRI/mrsim
-    cd mrsim
+    git clone [email protected]:INFN-MRI/torchsim
+    cd torchsim
     pip install -e .[dev,test,doc]
 
 

docs/api.rst

@@ -9,8 +9,8 @@ Base classes and routines for MR simulator implementation.
    :toctree: generated
    :nosignatures:
 
-   mrsim.base.AbstractModel
-   mrsim.base.autocast
+   torchsim.base.AbstractModel
+   torchsim.base.autocast
 
 Parameter configuration
 ~~~~~~~~~~~~~~~~~~~~~~~
@@ -19,11 +19,11 @@ Parameter configuration
    :toctree: generated
    :nosignatures:
 
-   mrsim.base.prepare_environmental_parameters
-   mrsim.base.prepare_single_pool
-   mrsim.base.prepare_two_pool_bm
-   mrsim.base.prepare_two_pool_mt
-   mrsim.base.prepare_three_pool
+   torchsim.base.prepare_environmental_parameters
+   torchsim.base.prepare_single_pool
+   torchsim.base.prepare_two_pool_bm
+   torchsim.base.prepare_two_pool_mt
+   torchsim.base.prepare_three_pool
 
 Extended Phase Graphs
 ---------------------
@@ -33,9 +33,9 @@ Subroutines for Extended Phase Graphs based simulators.
    :toctree: generated
    :nosignatures:
 
-   mrsim.epg.states_matrix
-   mrsim.epg.get_signal
-   mrsim.epg.get_demodulated_signal
+   torchsim.epg.states_matrix
+   torchsim.epg.get_signal
+   torchsim.epg.get_demodulated_signal
 
 RF Pulses
 ~~~~~~~~~
@@ -44,16 +44,16 @@ RF Pulses
    :toctree: generated
    :nosignatures:
 
-   mrsim.epg.rf_pulse_op
-   mrsim.epg.phased_rf_pulse_op
-   mrsim.epg.multidrive_rf_pulse_op
-   mrsim.epg.phased_multidrive_rf_pulse_op
-   mrsim.epg.rf_pulse
+   torchsim.epg.rf_pulse_op
+   torchsim.epg.phased_rf_pulse_op
+   torchsim.epg.multidrive_rf_pulse_op
+   torchsim.epg.phased_multidrive_rf_pulse_op
+   torchsim.epg.rf_pulse
 
-   mrsim.epg.initialize_mt_sat
-   mrsim.epg.mt_sat_op
-   mrsim.epg.multidrive_mt_sat_op
-   mrsim.epg.mt_sat
+   torchsim.epg.initialize_mt_sat
+   torchsim.epg.mt_sat_op
+   torchsim.epg.multidrive_mt_sat_op
+   torchsim.epg.mt_sat
 
 Relaxation and Exchange
 ~~~~~~~~~~~~~~~~~~~~~~~
@@ -62,14 +62,14 @@ Relaxation and Exchange
    :toctree: generated
    :nosignatures:
 
-   mrsim.epg.longitudinal_relaxation_op
-   mrsim.epg.longitudinal_relaxation
-   mrsim.epg.longitudinal_relaxation_exchange_op
-   mrsim.epg.longitudinal_relaxation_exchange
-   mrsim.epg.transverse_relaxation_op
-   mrsim.epg.transverse_relaxation
-   mrsim.epg.transverse_relaxation_exchange_op
-   mrsim.epg.transverse_relaxation_exchange
+   torchsim.epg.longitudinal_relaxation_op
+   torchsim.epg.longitudinal_relaxation
+   torchsim.epg.longitudinal_relaxation_exchange_op
+   torchsim.epg.longitudinal_relaxation_exchange
+   torchsim.epg.transverse_relaxation_op
+   torchsim.epg.transverse_relaxation
+   torchsim.epg.transverse_relaxation_exchange_op
+   torchsim.epg.transverse_relaxation_exchange
 
 Gradient Dephasing
 ~~~~~~~~~~~~~~~~~~
@@ -78,8 +78,8 @@ Gradient Dephasing
    :toctree: generated
    :nosignatures:
 
-   mrsim.epg.shift
-   mrsim.epg.spoil  
+   torchsim.epg.shift
+   torchsim.epg.spoil  
 
 Magnetization Prep
 ~~~~~~~~~~~~~~~~~~
@@ -88,7 +88,7 @@ Magnetization Prep
    :toctree: generated
    :nosignatures:
 
-    mrsim.epg.adiabatic_inversion   
+    torchsim.epg.adiabatic_inversion   
 
 Flow and Diffusion
 ~~~~~~~~~~~~~~~~~~
@@ -97,10 +97,10 @@ Flow and Diffusion
    :toctree: generated
    :nosignatures:
 
-   mrsim.epg.diffusion_op
-   mrsim.epg.diffusion
-   mrsim.epg.flow_op
-   mrsim.epg.flow   
+   torchsim.epg.diffusion_op
+   torchsim.epg.diffusion
+   torchsim.epg.flow_op
+   torchsim.epg.flow   
 
 Signal Models
 -------------
@@ -113,8 +113,8 @@ Analytical
    :toctree: generated
    :nosignatures:  
 
-   mrsim.models.bSSFPModel
-   mrsim.models.SPGRModel
+   torchsim.models.bSSFPModel
+   torchsim.models.SPGRModel
 
 Iterative
 ~~~~~~~~~
@@ -123,10 +123,10 @@ Iterative
    :toctree: generated
    :nosignatures:  
 
-   mrsim.models.FSEModel
-   mrsim.models.MP2RAGEModel
-   mrsim.models.MPnRAGEModel
-   mrsim.models.MRFModel
+   torchsim.models.FSEModel
+   torchsim.models.MP2RAGEModel
+   torchsim.models.MPnRAGEModel
+   torchsim.models.MRFModel
 
 Functional
 ----------
@@ -139,8 +139,8 @@ Analytical
    :toctree: generated
    :nosignatures:  
 
-   mrsim.bssfp_sim
-   mrsim.spgr_sim
+   torchsim.bssfp_sim
+   torchsim.spgr_sim
 
 Iterative
 ~~~~~~~~~
@@ -149,10 +149,10 @@ Iterative
    :toctree: generated
    :nosignatures:  
 
-   mrsim.fse_sim
-   mrsim.mp2rage_sim
-   mrsim.mpnrage_sim
-   mrsim.mrf_sim
+   torchsim.fse_sim
+   torchsim.mp2rage_sim
+   torchsim.mpnrage_sim
+   torchsim.mrf_sim
 
 Miscellaneous
 -------------
@@ -162,7 +162,7 @@ Other simulation utilities.
    :toctree: generated
    :nosignatures:
 
-   mrsim.utils.b1rms
-   mrsim.utils.slice_prof
+   torchsim.utils.b1rms
+   torchsim.utils.slice_prof
 
 

docs/conf.py

@@ -21,9 +21,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "mrsim"
-copyright = "2024, MRSim Contributors"
-author = "MRSim Contributors"
+project = "torchsim"
+copyright = "2024, TorchSim Contributors"
+author = "TorchSim Contributors"
 
 # -- General configuration ---------------------------------------------------
 
@@ -73,9 +73,9 @@
 # -- Options for Sphinx Gallery ----------------------------------------------
 
 sphinx_gallery_conf = {
-    "doc_module": "mrsim",
+    "doc_module": "torchsim",
     "backreferences_dir": "generated/gallery_backreferences",
-    "reference_url": {"mrsim": None},
+    "reference_url": {"torchsim": None},
     "examples_dirs": ["../examples/"],
     "gallery_dirs": ["generated/autoexamples"],
     "filename_pattern": "/0",
@@ -84,7 +84,7 @@
     "within_subsection_order": "FileNameSortKey",
     "binder": {
         "org": "infn-mri",
-        "repo": "mrsim",
+        "repo": "torchsim",
         "branch": "gh-pages",
         "binderhub_url": "https://mybinder.org",
         "dependencies": [
@@ -115,7 +115,7 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 # html_static_path = ["_static"]
 html_theme_options = {
-    "repository_url": "https://github.com/INFN-MRI/mrsim",
+    "repository_url": "https://github.com/INFN-MRI/torchsim",
     "use_repository_button": True,
     "use_issues_button": True,
     "use_edit_page_button": True,
@@ -125,4 +125,4 @@
 
 # html_logo = "_static/logos/mri-nufft.png"
 # html_favicon = "_static/logos/mri-nufft-icon.png"
-html_title = "MRSim Documentation"
+html_title = "TorchSim Documentation"

docs/getting_started.rst

@@ -1,39 +1,39 @@
 Getting Started
 ===============
 
-Installing MRSim
------------------
+Installing TorchSim
+-------------------
 
-MRSim is available on PyPi
+TorchSim is available on PyPi
 
 .. code-block:: sh
 
-    pip install mrsim
+    pip install torchsim
 
 Development Version
 ~~~~~~~~~~~~~~~~~~~
 
-If you want to modifiy the mrsim code base
+If you want to modifiy the ``torchsim`` code base
 
 .. code-block:: sh
 
-    git clone https://github.com/INFN-MRI/mrsim
-    pip install -e ./mrsim[test, dev, doc]
+    git clone https://github.com/INFN-MRI/torchsim
+    pip install -e ./torchsim[test, dev, doc]
 
 
 Basic Usage
 ===========
-Using MRSim, we can quickly implement and run MR simulations.
+Using TorchSim, we can quickly implement and run MR simulations.
 We also provide pre-defined simulators for several applications:
 
 .. code-block:: python
     
     import numpy as np
-    import mrsim
+    import torchsim
     
     # generate a flip angle pattern
     flip = np.concatenate((np.linspace(5, 60.0, 300), np.linspace(60.0, 2.0, 300), np.ones(280)*2.0))
-    sig, jac = mrsim.mrf_sim(flip=flip, TR=10.0, T1=1000.0, T2=100.0, diff=("T1","T2"))
+    sig, jac = torchsim.mrf_sim(flip=flip, TR=10.0, T1=1000.0, T2=100.0, diff=("T1","T2"))
     
 This way we obtained the forward pass signal (``sig``) as well as the jacobian
 calculated with respect to ``T1`` and ``T2``.