api -> function_reference

DIDSR · May 28, 2024 · b1ec0fb · b1ec0fb
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diff --git a/docs/source/api.rst → docs/source/function_reference.rst b/docs/source/api.rst → docs/source/function_reference.rst
@@ -1,5 +1,5 @@
-API
-===
+Function Reference
+==================
 
 Reference page
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -87,7 +87,7 @@ Contents
    usage
    notebooks/00_running_simulations
    notebooks/02_pediatric_denoising_evaluation
-   api
+   function_reference
    contributing
    faq
 

diff --git a/docs/source/notebooks/00_running_simulations.ipynb b/docs/source/notebooks/00_running_simulations.ipynb
@@ -28,7 +28,7 @@
    "source": [
     "## Individual Simulations\n",
     "\n",
-    "The main tool for running individual simulations is the [CTobj class](https://pediatriciqphantoms.readthedocs.io/en/latest/api.html#pediatricIQphantoms.CTobj) which both holds the key parameters for running and describing the scan as well as having methods to [run the scan](https://pediatriciqphantoms.readthedocs.io/en/latest/api.html#pediatricIQphantoms.CTobj.run) and [write the output to dicom](https://pediatriciqphantoms.readthedocs.io/en/latest/api.html#pediatricIQphantoms.CTobj.write_to_dicom)"
+    "The main tool for running individual simulations is the [CTobj class](https://pediatriciqphantoms.readthedocs.io/en/latest/function_reference.html#pediatricIQphantoms.CTobj) which both holds the key parameters for running and describing the scan as well as having methods to [run the scan](https://pediatriciqphantoms.readthedocs.io/en/latest/api.html#pediatricIQphantoms.CTobj.run) and [write the output to dicom](https://pediatriciqphantoms.readthedocs.io/en/latest/api.html#pediatricIQphantoms.CTobj.write_to_dicom)"
    ]
   },
   {
@@ -611,9 +611,9 @@
     "\n",
     "In MIRT convolution kernels are specified as `<window function>,<cutoff frequency mm>` for example a typical sharp kernel can be defined as 'hanning,2.05' where a [Hann window](https://en.wikipedia.org/wiki/Hann_function) with a cuffoff ([MTF](https://www.sciencedirect.com/topics/physics-and-astronomy/modulation-transfer-function#:~:text=The%20modulation%20transfer%20function%20(MTF,gets%20transferred%20to%20the%20image.)=0) frequency of 2.05 mm. The table below provides a few Siemen's equivalent kernels based upon matching 50% and 10% MTF cutoffs ([Zeng et al 2022](http://onlinelibrary.wiley.com/doi/abs/10.1002/mp.15430)).\n",
     "\n",
-    "| Description | MIRT         | Siemen's Equivalent |\r\n",
-    "|:-----------:|--------------|---------------------|\r\n",
-    "| Sharp       | hanning,2.05 | D45                 |\r\n",
+    "| Description | MIRT         | Siemen's Equivalent |\n",
+    "|:-----------:|--------------|---------------------|\n",
+    "| Sharp       | hanning,2.05 | D45                 |\n",
     "| Smooth      | hanning,0.85 | B30               \n",
     "\n",
     "The following experiment runs simulations on increasingly higher cutoff frequency kernels ranging from smooth to sharp.  |"
@@ -1719,7 +1719,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "For this example we will use [test.toml](../tests/configs/test.toml) as quick example"
+    "For this example we will use [sample_config_file.toml](sample_config_file.toml) as quick example"
    ]
   },
   {
@@ -2030,7 +2030,7 @@
     "\n",
     "In this notebook we walked through how to run [individual simulations](#Individual-Simulations) and [batched simulations](#Batch-Mode-Simulations) interactively as well as how to run and modify configuration files to be run noninteractively using the command line interface.\n",
     "\n",
-    "**Next** see the notebook on [viewing the simulation images](./01_viewing_images.ipynb)"
+    "**Next** see the notebook on [viewing the simulation images](https://github.com/DIDSR/pediatricIQphantoms/blob/main/notebooks/01_viewing_images.ipynb)"
    ]
   }
  ],

diff --git a/docs/source/notebooks/02_pediatric_denoising_evaluation.ipynb b/docs/source/notebooks/02_pediatric_denoising_evaluation.ipynb
@@ -1044,7 +1044,7 @@
    "source": [
     "## Conclusions\n",
     "\n",
-    "This concludes our worked examples. Next you can refer to the [API guide](https://pediatriciqphantoms.readthedocs.io/en/latest/api.html) for more detailed function documentation or [consider contributing the package](https://pediatriciqphantoms.readthedocs.io/en/latest/contributing.html).\n",
+    "This concludes our worked examples. Next you can refer to the [API guide](https://pediatriciqphantoms.readthedocs.io/en/latest/function_reference.html) for more detailed function documentation or [consider contributing the package](https://pediatriciqphantoms.readthedocs.io/en/latest/contributing.html).\n",
     "\n",
     "**Further Steps**\n",
     "\n",

diff --git a/docs/source/usage.rst b/docs/source/usage.rst
@@ -102,7 +102,7 @@ Viewing images
 
 The outputs of the simulation are `DICOM <https://en.wikipedia.org/wiki/DICOM>`_ CT images. The notebook `01_viewing_images.ipynb <https://github.com/DIDSR/pediatricIQphantoms/blob/main/notebooks/01_viewing_images.ipynb>`_ discusses ways to view and interact with DICOM images produced in `00_running_simulations.ipynb <https://github.com/DIDSR/pediatricIQphantoms/blob/main/notebooks/00_running_simulations.ipynb>`_
 
-`run_batch_sim <https://pediatriciqphantoms.readthedocs.io/en/latest/api.html#pediatricIQphantoms.run_batch_sim>`_ outputs simulated datasets in the following directory structure:
+`run_batch_sim <https://pediatriciqphantoms.readthedocs.io/en/latest/function_reference.html#pediatricIQphantoms.run_batch_sim>`_ outputs simulated datasets in the following directory structure:
 
 .. code-block:: shell
 
@@ -151,7 +151,7 @@ Examples of other viewers:
 Conclusions
 -----------
 
-This section introduced several ways to interact with pediatricIQphantom simulation tools and view the DICOM images produced by `run_batch_sim <https://pediatriciqphantoms.readthedocs.io/en/latest/api.html#pediatricIQphantoms.run_batch_sim>`_. 
+This section introduced several ways to interact with pediatricIQphantom simulation tools and view the DICOM images produced by `run_batch_sim <https://pediatriciqphantoms.readthedocs.io/en/latest/function_reference.html#pediatricIQphantoms.run_batch_sim>`_. 
 
 **Next** see the notebooks for practical examples `00_running_simulations.ipynb <https://github.com/DIDSR/pediatricIQphantoms/blob/main/notebooks/00_running_simulations.ipynb>`_
 

diff --git a/notebooks/00_running_simulations.ipynb b/notebooks/00_running_simulations.ipynb
@@ -28,7 +28,7 @@
    "source": [
     "## Individual Simulations\n",
     "\n",
-    "The main tool for running individual simulations is the [CTobj class](https://pediatriciqphantoms.readthedocs.io/en/latest/api.html#pediatricIQphantoms.CTobj) which both holds the key parameters for running and describing the scan as well as having methods to [run the scan](https://pediatriciqphantoms.readthedocs.io/en/latest/api.html#pediatricIQphantoms.CTobj.run) and [write the output to dicom](https://pediatriciqphantoms.readthedocs.io/en/latest/api.html#pediatricIQphantoms.CTobj.write_to_dicom)"
+    "The main tool for running individual simulations is the [CTobj class](https://pediatriciqphantoms.readthedocs.io/en/latest/function_reference.html#pediatricIQphantoms.CTobj) which both holds the key parameters for running and describing the scan as well as having methods to [run the scan](https://pediatriciqphantoms.readthedocs.io/en/latest/function_reference.html#pediatricIQphantoms.CTobj.run) and [write the output to dicom](https://pediatriciqphantoms.readthedocs.io/en/latest/function_reference.html#pediatricIQphantoms.CTobj.write_to_dicom)"
    ]
   },
   {
@@ -86,7 +86,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "You can also experiment with changing the lesion size for different phantoms, note CCT189 expects a length 4 list since the lesions are each different sizes, whereas CTP404 takes a single values since all inserts are equally sized. See [documentation](https://pediatriciqphantoms.readthedocs.io/en/latest/api.html#pediatricIQphantoms.run_batch_sim) for details.\n",
+    "You can also experiment with changing the lesion size for different phantoms, note CCT189 expects a length 4 list since the lesions are each different sizes, whereas CTP404 takes a single values since all inserts are equally sized. See [documentation](https://pediatriciqphantoms.readthedocs.io/en/latest/function_reference.html#pediatricIQphantoms.run_batch_sim) for details.\n",
     "```python\n",
     "import numpy as np\n",
     "lesion_diameter = np.array([0.015, 0.025, 0.035, 0.05])*2 # in order of 14 HU, 7 HU, 5 HU, and 3 HU\n",
@@ -233,7 +233,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The [`CTobj`](https://pediatriciqphantoms.readthedocs.io/en/latest/api.html#pediatricIQphantoms.CTobj) ooject also holds the `groundtruth` attribute following the reconstruction"
+    "The [`CTobj`](https://pediatriciqphantoms.readthedocs.io/en/latest/function_reference.html#pediatricIQphantoms.CTobj) ooject also holds the `groundtruth` attribute following the reconstruction"
    ]
   },
   {

diff --git a/notebooks/02_pediatric_denoising_evaluation.ipynb b/notebooks/02_pediatric_denoising_evaluation.ipynb
@@ -1044,7 +1044,7 @@
    "source": [
     "## Conclusions\n",
     "\n",
-    "This concludes our worked examples. Next you can refer to the [API guide](https://pediatriciqphantoms.readthedocs.io/en/latest/api.html) for more detailed function documentation or [consider contributing the package](https://pediatriciqphantoms.readthedocs.io/en/latest/contributing.html).\n",
+    "This concludes our worked examples. Next you can refer to the [API guide](https://pediatriciqphantoms.readthedocs.io/en/latest/function_reference.html) for more detailed function documentation or [consider contributing the package](https://pediatriciqphantoms.readthedocs.io/en/latest/contributing.html).\n",
     "\n",
     "**Further Steps**\n",
     "\n",

diff --git a/src/pediatricIQphantoms/make_phantoms.py b/src/pediatricIQphantoms/make_phantoms.py
@@ -327,7 +327,7 @@ def run_batch_sim(image_directory: str, model=['MITA-LCD'], diameter=[200], full
     :param dose_level: Optional list, units of photons
     :param verbose: Optional bool, whether to print update information
 
-    See `CTobj` for remaining **kwargs keyword arguments
+    See `CTobj` for remaining keyword arguments
     """
     image_directory = Path(os.path.abspath(image_directory))
     print(image_directory)