acjak · albusdemens · May 10, 2017 · May 10, 2017 · May 11, 2017 · May 11, 2017
diff --git a/.gitignore b/.gitignore
@@ -1 +1,11 @@
+*.DS_Store
+
+lib/.DS_Store
+
 *.pyc
+
+*.npy
+
+*.vtk
+
+*.jpg
diff --git a/LICENSE b/LICENSE
diff --git a/Manual_Recon3D.pdf b/Manual_Recon3D.pdf
diff --git a/Manual_files/ASTRA_recon3d_geom.png b/Manual_files/ASTRA_recon3d_geom.png
diff --git a/Manual_files/Animation.png b/Manual_files/Animation.png
diff --git a/Manual_files/Background_characterization.png b/Manual_files/Background_characterization.png
diff --git a/Manual_files/Comparison_ART_recon3d.png b/Manual_files/Comparison_ART_recon3d.png
diff --git a/Manual_files/Distr_I_int.png b/Manual_files/Distr_I_int.png
diff --git a/Manual_files/Estimate_CM.png b/Manual_files/Estimate_CM.png
diff --git a/Manual_files/I_before_after_normalization.png b/Manual_files/I_before_after_normalization.png
diff --git a/Manual_files/Img_cleaning.bib b/Manual_files/Img_cleaning.bib
@@ -0,0 +1,40 @@
+@article{henning_joac,
+  author={Poulsen, Henning Friis and et al.},
+  journal={In preparation},
+  year = 2017
+}
+
+@article{knudsen2013fabio,
+  title="{FabIO: easy access to two-dimensional X-ray detector images in Python}",
+  author={Knudsen, Erik B and S{\o}rensen, Henning O and Wright, Jonathan P and Goret, Gaeel and Kieffer, J{\'e}r{\^o}me},
+  journal={Journal of Applied Crystallography},
+  volume={46},
+  number={2},
+  pages={537--539},
+  year={2013},
+  publisher={International Union of Crystallography}
+}
+
+@article{dfxrm_nat_comm,
+  title="{Dark-field X-ray microscopy for multiscale structural characterization}",
+  author={Simons, Hugh and King, A and Ludwig, W and Detlefs, C and Pantleon, Wolfgang and Schmidt, S{\o}ren and Snigireva, I and Snigirev, A and Poulsen, Henning Friis},
+  journal={Nature Communications},
+  volume={6},
+  year={2015},
+  publisher={Nature Publishing Group}
+}
+
+@Misc{Recon3D_git,
+author =   {Cereser, Alberto and Anders, Clemens Jakobsen},
+title =    {Recon3D - software for {\footnotesize{3D}} reconstruction of topo-tomographic datasets from {\footnotesize{ID06}} at {\footnotesize{ESRF}}},
+howpublished = {\url{https://github.com/albusdemens/Recon3D}},
+year = {2016--2017}
+}
+
+@book{image_book,
+    author    = "Russ, C. J.",
+    title     = "The Image Processing Handbook",
+    year      = "2016",
+    publisher = "CRC Press",
+    address   = "Boca Raton, Florida"
+}
diff --git a/Manual_files/Img_cleaning.tex b/Manual_files/Img_cleaning.tex
diff --git a/Manual_files/Img_one_proj.png b/Manual_files/Img_one_proj.png
diff --git a/Manual_files/LICENSE b/Manual_files/LICENSE
@@ -0,0 +1,5 @@
+All files contained herein are licensed under the 
+Creative Commons Attribution-NonCommercial-Sharealike 3.0 License
+unless explictly marked otherwise.
+
+Information about this license can be found here: http://creativecommons.org/licenses/by-nc-sa/3.0/
diff --git a/Manual_files/Manual_DFXRM_software.bib b/Manual_files/Manual_DFXRM_software.bib
@@ -0,0 +1,83 @@
+@article{van2015astra,
+  title={The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography},
+  author={van Aarle, Wim and Palenstijn, Willem Jan and De Beenhouwer, Jan and Altantzis, Thomas and Bals, Sara and Batenburg, K Joost and Sijbers, Jan},
+  journal={Ultramicroscopy},
+  volume={157},
+  pages={35--47},
+  year={2015},
+  publisher={Elsevier}
+}
+
+@article{van2016fast,
+  title={Fast and flexible X-ray tomography using the ASTRA toolbox},
+  author={van Aarle, Wim and Palenstijn, Willem Jan and Cant, Jeroen and Janssens, Eline and Bleichrodt, Folkert and Dabravolski, Andrei and De Beenhouwer, Jan and Batenburg, K Joost and Sijbers, Jan},
+  journal={Optics express},
+  volume={24},
+  number={22},
+  pages={25129--25147},
+  year={2016},
+  publisher={Optical Society of America}
+}
+
+@article{laroque2008accurate,
+  title={Accurate image reconstruction from few-view and limited-angle data in diffraction tomography},
+  author={LaRoque, Samuel J and Sidky, Emil Y and Pan, Xiaochuan},
+  journal={JOSA A},
+  volume={25},
+  number={7},
+  pages={1772--1782},
+  year={2008},
+  publisher={Optical Society of America}
+}
+
+@TECHREPORT{report_jette_anders,
+  AUTHOR={Oddershede, Jette and C. Jakobsen, Anders},
+  TITLE="{3D reconstruction of {\footnotesize{DFXRM}} - derivation and implementation}",
+  INSTITUTION={DTU Physics},
+  MONTH={October},
+  YEAR={2016},
+}
+
+@article{henning_joac,
+  author={Poulsen, Henning Friis and C. Jakobsen, Anders and Simons, Hugh and R. Ahl, Sonja and Cook, P. K. and Deflets, Carsten.},
+  title="{X-ray diffraction microscopy based on refractive optics}",
+  journal={Journal of Applied Crystallography}, 
+  volume = {50},
+  number = {5},
+  year = 2017
+}
+
+@article{knudsen2013fabio,
+  title="{FabIO: easy access to two-dimensional X-ray detector images in Python}",
+  author={Knudsen, Erik B and S{\o}rensen, Henning O and Wright, Jonathan P and Goret, Gaeel and Kieffer, J{\'e}r{\^o}me},
+  journal={Journal of Applied Crystallography},
+  volume={46},
+  number={2},
+  pages={537--539},
+  year={2013},
+  publisher={International Union of Crystallography}
+}
+
+@article{dfxrm_nat_comm,
+  title="{Dark-field X-ray microscopy for multiscale structural characterization}",
+  author={Simons, Hugh and King, A and Ludwig, W and Detlefs, C and Pantleon, Wolfgang and Schmidt, S{\o}ren and Snigireva, I and Snigirev, A and Poulsen, Henning Friis},
+  journal={Nature Communications},
+  volume={6},
+  year={2015},
+  publisher={Nature Publishing Group}
+}
+
+@Misc{Recon3D_git,
+author =   {Cereser, Alberto and Anders, Clemens Jakobsen},
+title =    {Recon3D - software for {\footnotesize{3D}} reconstruction of topo-tomographic datasets from {\footnotesize{ID06}} at {\footnotesize{ESRF}}},
+howpublished = {\url{https://github.com/albusdemens/Recon3D}},
+year = {2016--2017}
+}
+
+@book{image_book,
+    author    = "Russ, C. J.",
+    title     = "The Image Processing Handbook",
+    year      = "2016",
+    publisher = "CRC Press",
+    address   = "Boca Raton, Florida"
+}