Fix links; add link to code

project.md

@@ -9,10 +9,19 @@ title: Final Project
 
 - [Radon Transform](http://www-math.mit.edu/~helgason/Radonbook.pdf) by Sigurdur Helgason
 - [Robust Uncertainty Principles: Exact Signal Reconstruction from Highly Incomplete Frequency
-  Information](../assets/pdf/2004_Candes_Romberg_Tao.pdf) by Candes, Romberg, and Tao
-- [Total Variation and Tomographic Imaging from Projections](../assets/pdf/2011_hansen_jorgensen.pdf)
+  Information](assets/pdf/2004_Candes_Romberg_Tao.pdf) by Candes, Romberg, and Tao
+- [Total Variation and Tomographic Imaging from Projections](assets/pdf/2011_Hansen_Jorgensen.pdf)
   by Hansen and Jørgensen
 
+## Code
+
+All my code is in this [repo](https://gitlab.cba.mit.edu/erik/funky_ct/tree/develop), named in honor
+of the [Radon transform](https://en.wikipedia.org/wiki/Radon_transform)'s more eccentric
+[cousin](https://en.wikipedia.org/wiki/Funk_transform). Building requires a modern C++ compiler and
+cmake. [Libpng](http://www.libpng.org/pub/png/libpng.html) must be installed as well. All told it's
+about 1,800 lines (excluding third party code), but there's some unnecessary duplication in there
+since I've been favoring velocity over hygiene.
+
 
 ## Fourier Reconstruction
 
@@ -30,7 +39,7 @@ $$
 p(x) = \int_\mathbb{R} f(x, y) dy
 $$
 
-Meanwhile, the [Fourier transform](../notes/fourier_transform.html) of $$f$$ is
+Meanwhile, the [Fourier transform](notes/fourier_transform.html) of $$f$$ is
 
 $$
 \hat{f}(u, v)
@@ -86,7 +95,7 @@ First, we'll want our Fourier transforms to be discrete Fourier transforms (DFTs
 continuous and discrete Fourier transforms are effectively interchangeable, as long as the functions
 we work with are mostly spatially and bandwidth limited, and we take an appropriate number of
 appropriately spaced samples. You can read more about these requirements
-[here](../notes/fourier_series.html).
+[here](notes/fourier_series.html).
 
 Second, since we combine the DFTs of the projections radially, we'll end up with samples (of the 2D
 Fourier transform of our image) on a polar grid rather than a cartesian one. So we'll have to
@@ -105,18 +114,18 @@ I used [FFTW](http://www.fftw.org/) to compute Fourier transforms. It's written
 I started with this image of a
 [brain](https://commons.wikimedia.org/wiki/File:FMRI_coronal_scan.jpg) from Wikimedia Commons.
 
-![brain](../assets/img/project_brain.png)
+![brain](assets/img/project_brain.png)
 
 Fourier reconstruction produces a nice [sinogram](https://en.wikipedia.org/wiki/Radon_transform).
 Each row is one projection, with angle going from 0 at the top to $$\pi$$ at the bottom, and $$r =
 0$$ down the middle column. You can clearly see the skull (a roughly circular feature) unwrapped to
 a line on the left side of the sinogram.
 
-![sinogram](../assets/img/project_sinogram.png)
+![sinogram](assets/img/project_sinogram.png)
 
 The reconstruction, however, isn't so clean.
 
-![brain](../assets/img/project_fourier_reconstruction.png)
+![brain](assets/img/project_fourier_reconstruction.png)
 
 The Fourier library I'm using is solid (and indeed it reproduces images very well even after
 repeated applications), so the error must be coming from my interpolation code. Indeed, the high
@@ -131,12 +140,12 @@ anyway so I'll move on.
 
 I got a number of interesting failures before getting my code to work correctly.
 
-![outtake](../assets/img/project_cool_1.png)
-![outtake](../assets/img/project_cool_2.png)
-![outtake](../assets/img/project_cool_3.png)
-![outtake](../assets/img/project_cool_4.png)
+![outtake](assets/img/project_cool_1.png)
+![outtake](assets/img/project_cool_2.png)
+![outtake](assets/img/project_cool_3.png)
+![outtake](assets/img/project_cool_4.png)
 
-These all started as attempts to project and reconstruct a [disk](../notes/fourier_examples.html),
+These all started as attempts to project and reconstruct a [disk](notes/fourier_examples.html),
 though I did experiment once interesting mistakes started happening. They mostly result from
 indexing errors and an issue with my integration with FFTW. The latter problem relates to the
 periodicity of discrete Fourier transforms and the resulting ambiguity in frequency interpretation.
@@ -148,13 +157,13 @@ For this application it's very important that the center of the polar coordinate
 resampling is right at the DC sample. So though the raw Fourier transform of the image looks like
 this (real and imaginary parts shown separately),
 
-![transform](../assets/img/project_transform_swapped_re.png)
-![transform](../assets/img/project_transform_swapped_im.png)
+![transform](assets/img/project_transform_swapped_re.png)
+![transform](assets/img/project_transform_swapped_im.png)
 
 we want to permute the quadrants so that it looks like this:
 
-![transform](../assets/img/project_transform_re.png)
-![transform](../assets/img/project_transform_im.png)
+![transform](assets/img/project_transform_re.png)
+![transform](assets/img/project_transform_im.png)
 
 Then the center of the image can be the center of the polar coordinate system. (Note: to make these
 I linearly mapped the full range of each image to [1, e], then applied the natural logarithm. So
@@ -250,17 +259,17 @@ I again use [FFTW](http://www.fftw.org/) for Fourier transforms. For interpolati
 sample to the left of the desired location, and for integration I just use a left Riemann sum. Even
 with these lazy techniques, the reconstruction looks quite good.
 
-![brain](../assets/img/project_fbp_reconstruction.png)
+![brain](assets/img/project_fbp_reconstruction.png)
 
 
 ## Total Variation / Compressed Sensing
 
 Unfortunately this is still a work in progress. I started implementing a [modern
-approach](../assets/pdf/2011_hansen_jorgensen.pdf), but found I didn't have enough background to
+approach](assets/pdf/2011_hansen_jorgensen.pdf), but found I didn't have enough background to
 make it work. They gloss over some details that I tried to get around with brute force, only to find
 that the resulting problem was computationally intractable. So yesterday I started over,
 re-implementing results from one of the original compressed sensing
-[papers](../assets/pdf/2004_Candes_Romberg_Tao.pdf). However I did learn some things from my failed
+[papers](assets/pdf/2004_Candes_Romberg_Tao.pdf). However I did learn some things from my failed
 attempts...
 
 
@@ -278,24 +287,24 @@ of the Fourier and filtered back projection algorithms implemented as matrices.
 and create a sinogram with a single matrix multiplication. As mentioned the matrices are huge, so
 here I'll work with a 32 by 32 brain image.
 
-![dft](../assets/img/project_tiny_brain.png)
+![dft](assets/img/project_tiny_brain.png)
 
 The DFTs were easy. Very similar to the cosine transform we used in the last problem set.
 
-![dft](../assets/img/project_matrix_dft_re.png)
-![dft](../assets/img/project_matrix_dft_im.png)
+![dft](assets/img/project_matrix_dft_re.png)
+![dft](assets/img/project_matrix_dft_im.png)
 
 To construct the polar interpolation matrix, I rewrote my interpolation routine to drop the weights
 it calculated in the appropriate entries in a matrix rather than summing things up as it goes. These
 weights depend on the type of interpolation used and the sizes of the images involved.
 
-![dft](../assets/img/project_matrix_polar_re.png)
-![dft](../assets/img/project_matrix_polar_im.png)
+![dft](assets/img/project_matrix_polar_re.png)
+![dft](assets/img/project_matrix_polar_im.png)
 
 Finally it's just some (inverse) DFTs to get the sinogram. They can all be expressed simultaneously
 in one matrix.
 
-![dft](../assets/img/project_matrix_sinogram.png)
+![dft](assets/img/project_matrix_sinogram.png)
 
 I bump up the pixel count for the polar projections so that the resampling doesn't lose as much
 information. Thus the final matrix that performs all three of these operations at once has
@@ -316,11 +325,11 @@ I scanned a 3d print that I made in [How to Make (almost)
 Anything](http://fab.cba.mit.edu/classes/863.18/CBA/people/erik/04_3d_printing_scanning/) last
 semester.
 
-![3d print](../assets/img/project_3d_print.jpg)
+![3d print](assets/img/project_3d_print.jpg)
 
 I reconstructed it using TomoPy's gridrec implementation.
 
-![3d print](../assets/img/project_3d_print_reconstruction.jpg)
+![3d print](assets/img/project_3d_print_reconstruction.jpg)
 
 The results aren't that great, so evidently the settings will require some tweaking. Ultimately I'd
 like to set up an easy to use TomoPy/ASTRA toolchain to use with CBA's CT scanner; this is just a