revisions in response to code review recommendations

README.rst

@@ -94,7 +94,7 @@ To run the `computational notebooks <https://github.com/DIDSR/pediatricIQphantom
 How to use this repo and the Pediatric IQ Phantoms
 --------------------------------------------------
 
-**pediatricIQphantoms** provides examples for how to use the pediatric IQ phantoms, (available to download and use directly from `Zenodo <https://zenodo.org/doi/10.5281/zenodo.10064035>`_) or generate new phantom instances using the provided `phantom generation functions <src/pediatricIQphantoms/make_phantoms.py>`_.
+**pediatricIQphantoms `Documentation`_** provides further details on the `rationale <https://pediatriciqphantoms.readthedocs.io/en/latest/usage.html#intended-purpose>`_, usage, and examples for how to use the pediatric IQ phantoms, (available to download and use directly from `Zenodo <https://zenodo.org/doi/10.5281/zenodo.10064035>`_) or generate new phantom instances using the provided `phantom generation functions <src/pediatricIQphantoms/make_phantoms.py>`_.
 
 Several examples are provided on how to use these functions:
 
@@ -114,9 +114,13 @@ Contribute
 Support
 -------
 
+For questions that cannot be addressed in the supporting `Documentation`_
+
 If you are having issues, please let us know.
 `brandon.nelson@fda.hhs.gov <mailto:brandon.nelson@fda.hhs.gov>`_; `rongping.zeng@fda.hhs.gov <rongping.zeng@fda.hhs.gov>`_
 
+.. _Documentation: https://pediatriciqphantoms.readthedocs.io/en/latest/
+
 Disclaimer
 ----------
 

configs/LCD.toml

@@ -0,0 +1,36 @@
+# LCD.toml
+
+[[simulation]]
+
+# directories
+image_directory = "/gpfs_projects/brandon.nelson/RSTs/LCD-CT"
+# phantoms
+model = ['MITA-LCD', 'uniform'] # <-- current options include ['CTP404', 'MITA-LCD', 'UNIFORM']
+diameter = [200] # <-- units in mm
+reference_diameter = 200 # <-- diameter in mm of the real phantom for comparison
+
+# acquisition
+framework = "MIRT" # CT simulation framework options include ['MIRT'] <https://github.com/JeffFessler/mirt>
+nsims = 200 # <-- number of simulations to perform with different noise instantiations
+ndetectors = 880           # number of detector columns (set it to be large enough to cover the projected FOV to avoid truncation)
+nangles = 1160 # <-- number of views in a rotation (na=1160 based on ZengEtAl2015-IEEE-NuclearScience-v62n5:"A Simple Low-Dose X-Ray CT Simulation From High-Dose Scan")
+aec_on = true # (aec built in to ped xcat) <-- 'aec' = automatic exposure control, when `true`, it ensures constant noise levels for all `patient_diameters` (see `reference_dose_level` for more info)
+add_noise = true # <-- if true adds Poisson noise, noise magnitude set by `reference_dose_level`, noise texture set by reconstructed field of view (currently fov = 110# patient_diameter) 
+full_dose = 3e5 # <-- units of photons per pixel
+dose_level = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0] # <-- units of photons in list
+
+# acquisition geometry # CT geometry (the following parameter values simulate Siemens Force) 
+sid = 595          #(mm) source-to-isocenter distance (value based on AAPM LDCT data dicom header)
+sdd = 1085.6          # source-to-detector distance
+# isocenter-to-detector distance dod = sdd - sid 
+
+detector_size = 1        # detector column size 
+detector_offset = 1.25    # lateral shift of detector
+
+# reconstruction
+fov = 340  # <-- FOV in mm of adult protocol used in scanning real physical phantom for comparison
+matrix_size = 512 # <-- reconstructed matrix size in pixels (square, equal on both sides)
+fbp_kernel = 'hanning,2.05' # 'hanning,xxx', xxx = the cutoff frequency, see fbp2_window.m in MIRT for details.
+                        #'hanning,2.05' approximate a sharp kernel D45 in Siemens Force.
+                        #'hanning, 0.85' approximate a smooth kernel B30 in
+                        #Siemens Force.

docs/source/usage.rst

@@ -85,7 +85,7 @@ Finally by the fourth we repeat the previous simulation but with the second kern
 
     fbp_kernel = 'hanning,0.85'
 
-This is done in parsing the config files using the python `dict update method <https://docs.python.org/3/library/stdtypes.html?highlight=dict%20update#dict.update>`_ https://github.com/DIDSR/pediatricIQphantoms/blob/62a45930053502e8e9982af4b521fdd4eee314ed/make_phantoms.py#L56
+This is done in parsing the config files using the python `dict update method <https://docs.python.org/3/library/stdtypes.html?highlight=dict%20update#dict.update>`_ :py:func:`pediatricIQphantoms.make_phantoms`
 
 - Reproducing the `pediatricIQphantoms dataset <https://zenodo.org/doi/10.5281/zenodo.10064035>`_
 
@@ -95,7 +95,7 @@ This is done in parsing the config files using the python `dict update method <h
 
     make_phantoms configs/pediatricIQphantoms.toml
 
-Note that this example of the executable `make_phantoms` that is installed and added to your python after installing the `pediatricIQphantoms <https://github.com/DIDSR/pediatricIQphantoms>`_ python package (see `install instructions <https://pediatriciqphantoms.readthedocs.io/en/latest/index.html>`_ for details)
+Note that this example of the executable `make_phantoms` that is installed and added to your python after installing the `pediatricIQphantoms <https://github.com/DIDSR/pediatricIQphantoms>`_ python package (see `install instructions <https://pediatriciqphantoms.readthedocs.io/en/latest/index.html#installation>`_ for details)
 
 Viewing images
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notebooks/denoising/README

@@ -0,0 +1 @@
+This directory was cloned from https://github.com/SSinyu/RED-CNN/tree/master