Reorganize to prep for applying scientific-python cookie

.gitignore

@@ -5,4 +5,4 @@ env*
 *.pyc
 .vscode
 docs/_build/
-docs/_autosummary/
+docs/_autosummary/

LICENSE

@@ -657,4 +657,4 @@ the specific requirements.
 You should also get your employer (if you work as a programmer) or
 school, if any, to sign a "copyright disclaimer" for the program, if
 necessary. For more information on this, and how to apply and follow
-the GNU AGPL, see <https://www.gnu.org/licenses/>.
+the GNU AGPL, see <https://www.gnu.org/licenses/>.

README.rst

@@ -1,26 +1,50 @@
-****
 Home
-****
+========
 
-Open-pyFUS is a toolbox for planning and controlling focused ultrasound treatments. It generally replicates the functionality developed in the MATLAB `open-TFUS toolbox <https://github.com/OpenwaterHealth/opw_neuromod_sw>`_.
+``openlifu`` is a toolbox for planning and controlling focused
+ultrasound treatments. It generally replicates the functionality
+developed in the MATLAB `open-TFUS
+toolbox <https://github.com/OpenwaterHealth/opw_neuromod_sw>`__.
 
 Installation
 ------------
 
 Requirements
-^^^^^^^^^^^^
+~~~~~~~~~~~~
+
 Python 3.11
 
 Create Virtual Environment
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-``cd open_pyfus``
-``C:\Users\<uname>\AppData\Local\Programs\Python\Python311\python.exe -m venv env``
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Windows:
+
+.. code:: sh
+
+   C:\Users\<uname>\AppData\Local\Programs\Python\Python311\python.exe -m venv env
+   .\env\Scripts\activate
+
+Linux:
+
+.. code:: sh
+
+   python3.11 -m venv env
 
 Install project (editable)
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-``.\env\Scripts\activate``
-``pip install -e .``
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+With this repo as the working directory:
+
+.. code:: sh
+
+   pip install -e .
 
 Disclaimer
 ----------
-CAUTION - Investigational device. Limited by Federal (or United States) law to investigational use. The system described here has *not* been evaluated by the FDA and is not designed for the treatment or diagnosis of any disease. It is provided AS-IS, with no warranties. User assumes all liability and responsibility for identifying and mitigating risks associated with using this software.
+
+CAUTION - Investigational device. Limited by Federal (or United States)
+law to investigational use. The system described here has *not* been
+evaluated by the FDA and is not designed for the treatment or diagnosis
+of any disease. It is provided AS-IS, with no warranties. User assumes
+all liability and responsibility for identifying and mitigating risks
+associated with using this software.

docs/_templates/custom-class-template.rst

@@ -3,5 +3,5 @@
 .. currentmodule:: {{ module }}
 
 .. autoclass:: {{ objname }}
-   :members:                      
-   :show-inheritance:                                     
+   :members:
+   :show-inheritance:

docs/_templates/custom-module-template.rst

@@ -1,7 +1,7 @@
 {{ fullname | escape | underline}}
 
 .. automodule:: {{ fullname }}
-  
+
    {% block attributes %}
    {% if attributes %}
    .. rubric:: Module Attributes
@@ -63,4 +63,4 @@
    {{ item }}
 {%- endfor %}
 {% endif %}
-{% endblock %}
+{% endblock %}

docs/api.rst

@@ -1,12 +1,11 @@
 API Reference
 =============
 
-The top-level module containing most of the code is `pyfus`
+The top-level module containing most of the code is ``openlifu``
 
-.. autosummary:: 
+.. autosummary::
     :toctree: _autosummary
     :template: custom-module-template.rst
     :recursive:
 
-    pyfus
-
+    openlifu

docs/conf.py

@@ -6,7 +6,7 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'Open-pyFUS'
+project = 'OpenLIFU-Python'
 copyright = '2023, Openwater'
 author = 'Openwater'
 release = '0.1'

docs/includeme.rst

@@ -1 +1 @@
-.. include:: ../README.rst
+.. include:: ../README.rst

docs/index.rst

@@ -1,10 +1,10 @@
-Welcome to open-PYFUS's documentation!
-=========================================   
+Welcome to openlifu's documentation!
+=========================================
 
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
-   
+
    includeme
    api
 

test_notebooks/test_first.ipynb → notebooks/test_first.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "If you have my modified version of k-wave-python, install it with `pip install -e .` from the `k-wave-python` directory. If you don't have my modified version, you can install the original version with `pip install k-wave-python`. If you are using the original version, be sure to set `USE_GRIDWEIGHTS` to `False` in order to prevent `open_pyfus` from trying to use a nonexistent interface for loading the gridweights. \n",
     "\n",
-    "Also, if you are using the original version, import `pyfus` takes _way_ longer (45s on my PC), presumably hanging on `import kwave`. For some reason, it wants to re-download the binaries every time, even though they are already present in the the installation directory. I've opened an issue on this: https://github.com/waltsims/k-wave-python/issues/366."
+    "Also, if you are using the original version, import `openlifu` takes _way_ longer (45s on my PC), presumably hanging on `import kwave`. For some reason, it wants to re-download the binaries every time, even though they are already present in the the installation directory. I've opened an issue on this: https://github.com/waltsims/k-wave-python/issues/366."
    ]
   },
   {
@@ -28,7 +28,7 @@
     "formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')\n",
     "handler.setFormatter(formatter)\n",
     "root.addHandler(handler)\n",
-    "import pyfus\n",
+    "import openlifu\n",
     "import numpy as np"
    ]
   },
@@ -55,7 +55,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "arr = pyfus.Transducer.gen_matrix_array(nx=8, ny=8, pitch=4, kerf=.5, units=\"mm\", impulse_response=1e5)\n",
+    "arr = openlifu.Transducer.gen_matrix_array(nx=8, ny=8, pitch=4, kerf=.5, units=\"mm\", impulse_response=1e5)\n",
     "arr.draw()"
    ]
   },
@@ -72,11 +72,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pulse = pyfus.Pulse(frequency=400e3, duration=3/400e3)\n",
-    "sequence = pyfus.Sequence()\n",
-    "focal_pattern = pyfus.focal_patterns.Wheel(center=True, spoke_radius=5, num_spokes=5)\n",
-    "sim_setup = pyfus.SimSetup(dt=2e-7, t_end=100e-6)\n",
-    "protocol = pyfus.Protocol(\n",
+    "pulse = openlifu.Pulse(frequency=400e3, duration=3/400e3)\n",
+    "sequence = openlifu.Sequence()\n",
+    "focal_pattern = openlifu.focal_patterns.Wheel(center=True, spoke_radius=5, num_spokes=5)\n",
+    "sim_setup = openlifu.SimSetup(dt=2e-7, t_end=100e-6)\n",
+    "protocol = openlifu.Protocol(\n",
     "    pulse=pulse,\n",
     "    sequence=sequence,\n",
     "    focal_pattern=focal_pattern,\n",
@@ -96,7 +96,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pt = pyfus.Point(position=(0,0,30), units=\"mm\", radius=2)\n",
+    "pt = openlifu.Point(position=(0,0,30), units=\"mm\", radius=2)\n",
     "pts = protocol.focal_pattern.get_targets(pt)\n",
     "coords = protocol.sim_setup.get_coords()\n",
     "params = protocol.seg_method.ref_params(coords)\n",
@@ -116,7 +116,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ds = pyfus.sim.run_simulation(arr=arr, \n",
+    "ds = openlifu.sim.run_simulation(arr=arr, \n",
     "        params=params, \n",
     "        delays=delays,\n",
     "        apod= apod,\n",

test_notebooks/test_gridweights.ipynb → notebooks/test_gridweights.ipynb

@@ -8,7 +8,7 @@
    "source": [
     "import sys\n",
     "sys.path.append(R'C:\\Users\\pjh7\\git\\k-wave-python')\n",
-    "import pyfus\n",
+    "import openlifu\n",
     "from typing import List, Dict, Any, Tuple\n",
     "import logging\n",
     "import matplotlib.pyplot as plt\n",
@@ -40,7 +40,7 @@
    ],
    "source": [
     "\n",
-    "db = pyfus.database.Database(path=R'C:/Users/pjh7/Documents/dom/')\n",
+    "db = openlifu.database.Database(path=R'C:/Users/pjh7/Documents/dom/')\n",
     "arr = db.load_transducer('vermon')\n",
     "trans_matrix = np.array(\n",
     "    [[-1,   0,  0, 0],\n",
@@ -49,7 +49,7 @@
     "     [0, 0,  0, 1]])\n",
     "arr.rescale(\"mm\")\n",
     "arr.matrix = trans_matrix\n",
-    "pt = pyfus.geo.Point(position=(5,-60,-8), units=\"mm\", radius=2)\n",
+    "pt = openlifu.geo.Point(position=(5,-60,-8), units=\"mm\", radius=2)\n",
     "plan = db.load_plan('example_plan')\n",
     "plan.sim_grid.dt = 2e-7\n",
     "plan.sim_grid.t_end = 100e-6\n",
@@ -107,7 +107,7 @@
     }
    ],
    "source": [
-    "ds, output = pyfus.sim.run_simulation(arr=arr, \n",
+    "ds, output = openlifu.sim.run_simulation(arr=arr, \n",
     "               params=params, \n",
     "               delays=delays,\n",
     "               apod= apod,\n",
@@ -411,12 +411,12 @@
    "outputs": [],
    "source": [
     "\n",
-    "focal_pattern = pyfus.bf.RadialPattern(center=True, spoke_radius=5, num_spokes=5)\n",
-    "sim_grid = pyfus.bf.SimulationGrid(dt=2e-7, t_end=100e-6)\n",
-    "pulse = pyfus.bf.Pulse(frequency=400e3, duration=3/400e3)\n",
-    "sequence = pyfus.bf.Sequence()\n",
-    "bfp = pyfus.bf.BeamformingPlan()\n",
-    "plan = pyfus.plan.Plan(pulse=pulse,\n",
+    "focal_pattern = openlifu.bf.RadialPattern(center=True, spoke_radius=5, num_spokes=5)\n",
+    "sim_grid = openlifu.bf.SimulationGrid(dt=2e-7, t_end=100e-6)\n",
+    "pulse = openlifu.bf.Pulse(frequency=400e3, duration=3/400e3)\n",
+    "sequence = openlifu.bf.Sequence()\n",
+    "bfp = openlifu.bf.BeamformingPlan()\n",
+    "plan = openlifu.plan.Plan(pulse=pulse,\n",
     "                 sequence=sequence,\n",
     "                 focal_pattern=focal_pattern,\n",
     "                 sim_grid=sim_grid,\n",

test_notebooks/test_nifti.ipynb → notebooks/test_nifti.ipynb

@@ -10,7 +10,7 @@
     "slicer_exe = R\"C:\\Users\\pjh7\\AppData\\Local\\NA-MIC\\Slicer 5.2.2\\Slicer.exe\"\n",
     "import sys\n",
     "sys.path.append(modified_kwave_path)\n",
-    "import pyfus\n",
+    "import openlifu\n",
     "from typing import List, Dict, Any, Tuple\n",
     "import logging\n",
     "root = logging.getLogger()\n",
@@ -39,15 +39,15 @@
    ],
    "source": [
     "\n",
-    "arr = pyfus.Transducer.gen_matrix_array(nx=8, ny=8, pitch=4, kerf=.5, units=\"mm\", impulse_response=1e5)\n",
+    "arr = openlifu.Transducer.gen_matrix_array(nx=8, ny=8, pitch=4, kerf=.5, units=\"mm\", impulse_response=1e5)\n",
     "trans_matrix = np.array(\n",
     "    [[-1,   0,  0, 0],\n",
     "     [0, .05,  np.sqrt(1-.05**2), -105],\n",
     "     [0, np.sqrt(1-.05**2),  -.05, 5],\n",
     "     [0, 0,  0, 1]])\n",
     "arr.rescale(\"mm\")\n",
     "arr.matrix = trans_matrix\n",
-    "pt = pyfus.Point(position=(5,-60,-8), units=\"mm\", radius=2)"
+    "pt = openlifu.Point(position=(5,-60,-8), units=\"mm\", radius=2)"
    ]
   },
   {
@@ -56,11 +56,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pulse = pyfus.Pulse(frequency=400e3, duration=3/400e3)\n",
-    "sequence = pyfus.Sequence()\n",
-    "focal_pattern = pyfus.focal_patterns.Wheel(center=True, spoke_radius=5, num_spokes=5)\n",
-    "sim_setup = pyfus.SimSetup(dt=2e-7, t_end=100e-6)\n",
-    "protocol = pyfus.Protocol(\n",
+    "pulse = openlifu.Pulse(frequency=400e3, duration=3/400e3)\n",
+    "sequence = openlifu.Sequence()\n",
+    "focal_pattern = openlifu.focal_patterns.Wheel(center=True, spoke_radius=5, num_spokes=5)\n",
+    "sim_setup = openlifu.SimSetup(dt=2e-7, t_end=100e-6)\n",
+    "protocol = openlifu.Protocol(\n",
     "    pulse=pulse,\n",
     "    sequence=sequence,\n",
     "    focal_pattern=focal_pattern,\n",
@@ -112,7 +112,7 @@
     }
    ],
    "source": [
-    "ds = pyfus.sim.run_simulation(arr=arr, \n",
+    "ds = openlifu.sim.run_simulation(arr=arr, \n",
     "        params=params, \n",
     "        delays=delays,\n",
     "        apod= apod,\n",

test_notebooks/test_registers.ipynb → notebooks/test_registers.ipynb

@@ -6,7 +6,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pyfus.io.ustx import PulseProfile, DelayProfile, TxModule, Tx7332Registers, print_regs, TxArray, swap_byte_order\n",
+    "from openlifu.io.ustx import PulseProfile, DelayProfile, TxModule, Tx7332Registers, print_regs, TxArray, swap_byte_order\n",
     "import numpy as np"
    ]
   },

pyproject.toml

@@ -1,5 +1,5 @@
 [project]
-name = "open_pyfus"
+name = "openlifu"
 version = "0.1.0"
 description = "Openwater Focused Ultrasound Toolkit"
 dependencies = [
@@ -19,7 +19,3 @@ dependencies = [
 
 [tool.setuptools]
 include-package-data = false
-
-[tool.setuptools.packages.find]
-include = ["pyfus*"]
-exclude = ["test*", "env*"]