From 766cca404415cfc8ceac9897072b42cb95d370a1 Mon Sep 17 00:00:00 2001 From: Ibrahim Hadzic Date: Sat, 8 May 2021 20:51:58 +0200 Subject: [PATCH] init mkdocs documentation --- .gitignore | 2 ++ CONTRIBUTING.md | 1 + docs/README.md | 11 +++++++ docs/imgs/your_first_run_docker.png | Bin 0 -> 5487 bytes docs/index.md | 43 ++++++++++++++++++++++++++++ docs/installation.md | 42 +++++++++++++++++++++++++++ docs/tutorials/your_first_run.md | 25 ++++++++++++++++ mkdocs.yml | 9 ++++++ 8 files changed, 133 insertions(+) create mode 100644 CONTRIBUTING.md create mode 100644 docs/README.md create mode 100644 docs/imgs/your_first_run_docker.png create mode 100644 docs/index.md create mode 100644 docs/installation.md create mode 100644 docs/tutorials/your_first_run.md create mode 100644 mkdocs.yml diff --git a/.gitignore b/.gitignore index b529dcc..1eed167 100644 --- a/.gitignore +++ b/.gitignore @@ -125,3 +125,5 @@ results *.nrrd Untitled.ipynb core.* + +projects/maastro_lung_proton_cbct_to_ct/experiments/2d_vnet_local.yaml diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..b037922 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1 @@ +Wish to contribute? Here, you can find guidelines. \ No newline at end of file diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 0000000..3718d50 --- /dev/null +++ b/docs/README.md @@ -0,0 +1,11 @@ +# Documentation + +Our documentation is based on ![Mkdocs](https://github.com/mkdocs/mkdocs) + +The `/docs` folder contains pages of the documentation website, `/imgs` the media used in them. +Mkdocs is configured with `../mkdocs.yaml`, located in the root of the project. + +To host locally, run this command from the root of the project: +``` +mkdocs serve +``` \ No newline at end of file diff --git a/docs/imgs/your_first_run_docker.png b/docs/imgs/your_first_run_docker.png new file mode 100644 index 0000000000000000000000000000000000000000..0d591ae3b6873ed110dae29ba7192d6400c56699 GIT binary patch literal 5487 zcmYjV2{e@L`<_I$q)3YFTTEqNk~L)Cx5)5CmJB2NPEywFhHNAIKC(=VwXzdq9}U?V zgOPoZ_>V9BzW+J*dCz;^<++#Vey{7k-bg(iRT?TLDgXdLqpqfG003N+CY~!%kPwfP zH?ZCS0E2|OvZ9gC1$@@i#B!-CVg79NWX%~QMCaiVYaE|Dq#{@ScDDLdLyrJ*D|tQjuWj+n`IZPFfbKAoK!I;Iiee)W0s>O?S0 zv$h&YHQ2lfbW@6gM3)DR7Eo8Vrtc%BKr<|^ z>s}i1RZwZO&cmINd084NGR4_wQZ;y5bjBcUV8XiHR@sl``}4HOtq5pBT=fEiOOPsm zNMEoGIHGFME@Sko*0X>Y71Yf5AWxcRh|p^I(S7Ae-#b&@)j_ujH5>5N`1*yAI$phZ z@SgQ4rTJT3%)kE;Zq#*0IS&Z_KHy^93ZL3s!kp}sx^%VG&9tm=q6YGYy^m_XvuxCk zxK1v9uS|_Ic}8(}k>F3+&dImZR)Tw7Iy+9vsgX4XmyMiq zL`FrKacx5HPdw&1<*s36Tq;4Lc-l6F9j!T6UB?tTF_f-G-7&7CFG~WQ$x1UFA$gFt z?SE2}75|i4-C@~xsbdUblZ}D}(w1k^L$6Zap3lDH2lL+&IUP+r-1F>Zv+?M!v4Ne= z>v{#gT?-7g_crX~a9c)U0sRMVof9%{zh6toEpEnJgF2vP>HnSGK$h)3z{3 zCqAN*G1Q$^@RK5d^oUeqG5wv#)Z+$Fyxn*6lC~cgXXffhm=1^cAnwC7YJwdEE(7mC z@1nE~@+zzE3Bkx2wD0__vPrQu4JOh1`{5h>qg|T-U7wq;mdrDBcDhsKv+7IzB-zA2 z;-jz5DpD^?xU?8`)Y311F?*}|D@vY~+?nax1@jktmiz|TpGTl>hB2U`-M^w5(u9jI?(@PqfRLXKPmNV`HH4v}5J+{NQ-nnnP@VLpi0C_r=Q@a1V zu`o+Oe{FBrP>Kg73yI%aD0mbjBF0E&jl&AV{4K_0zI~~l+39MC&F$jI^pSH=8N0-9 zf9ty-TO%B!qG^n)l1O>{&BD+!fNep3BlT)uiGOlu1Pu`fcm|>10lYeO9rGBAvPk`p z3Cdq?sw1~VQ&cOM?V8h_N3ws{A&0i@M}l6utnK&H#s8euZjw>eCMdz`#O>I`CZ41| zvmZf4g<=*>bfS7|7M8FaZ+z!^w#S1@YjLyvJEd)W#n@q;E?rbhn4a^;l2N6;Ay{B~ zXvJjo4tQkyu}pT{ks-3Ev5*C&D=4dMkBBx|bbeofvxN^oJb8}|4!5`Ubw}4_XYFqt z?H%t9H)B9ZlW9Igy}i{)*&14t0O#r#6fYGQlzou$nBs+SWTDMPQiWL{X@lE6%MS*M zQ){3g+I3b;@x%cr)zSILMp}tb_@p{Y(?w~^=U9IF{zA}6>s%bB1mERm?8p3~Tj7xA zm+#4Btj_3yS90ihA6ZQhaGMg+1^L!jiK{LyqqFB&kt(EfN?EB^PSpi>Mc2vlxY73G zdyO{jqm>w3-U?TC*Jj&KAe}KKbX*uQzuRB=C##l_UF700`$Dst>cE}620TbL{h2(f zsXGUMe6)T1pligPOPvL#zn+;1Y2K1CI>_N^-W{x+tCYLvDP!p^GD>{|#||L*MY+3( zi9|3G_v(1I{o_W385eZ#$d)kJdG%c%6T78*P4oWRW;*S*s>_py5cj!$gNF-LM?g5) z`mdiIn!!gSelo-TzTU%heFw}zpYRzKAW^B}K(g!WT@dzl3H-$J&jVDJvgk{O4CO$z zAMf4e-g^n0G^7-73srVZrrg=db844EHT#UQK{OmqgnhndPtpI_Uw3GBn-(A!%yKXU zqVc&5zRauz8hIHVY~3TZKY9Gnsn|Gg76h*MdzrK@icS23*Mm=9{q;e{K^@U0$F0a% zu~we~A+uQelS(De`+ca8=DD?Ni}Vp)k|*uIeOo zCd_01c}%*aQk#V_Q9kX~VBuQ_J>hgbya~uL;M%mjg))GI*g7a4B2!zme7r)! z9#22}6S&K2+AC_q{4e(_P$r~Vrwx})0n@iLqhF7#**fxGsQCfRuA)BA@8=`-7j4N_H1nS7BuZ-OkS3N$U(q(Mw@pVzUk-S+0;R@K%|d~p*#naxo1sPA11_9JKJ4<|>fSM-w0M2x zVXvW|lM~{fPTNoZ0*`DB+TPYPePJ5lIxN;1-*6;n{<8z@o0g=R2rwr&H$EYL-twr> z4jLrp2Gw>nTQY}e#C5XDm$wY>%DA_%h;?bv(%-<@l2>{?l4KKgDa1;Y;d_&BSI~K5 zikxB|my}M{O!kVSvhzK-qFMq`v8k*MP8|gSwO$hShVU)E8-&Bk{i+M+l|ge~T}+oo z$J!y19PVaBJ!jF@f9NkE?dF{6z$*NE^K<4hn{6%nEJXohGd@0?gC>Zu$WYoz!23%yZF!#-OPTc`!-^B;H&LQz2hjR?I_I8C2eJE-H1sO?~lv! zE93k!=TNoX+I!pGHZ;Nn=;0_yd&}+KxX~ef#(N!-5hLizAquzQ`v{uq>U!dDZhdnS zR3=JeQc;p-%jH5?z3TP1Ye5v77{p}L-DjObY#`<^#Rem@!A{zDVS?O#xbUyzu@b#u z+rei3$rT(U#|F{M`vL_yhzBy461*olsh|J8B|D-JC;f)+nK(S?s09HIn<`l^V-W;h ziZaV008#Xn{UGUH)M3T}v$j z>$P3QiK~85?FlM$$X10qSjPpA3(DVe>}D}(t9q>^?1Q6AkhAcO(+&HS04aR$)?bFc z{y0mZy}m~~3#)1tH76~b@4AGC)IaKa|t`I=rt{GW`Wx+VDdvp)Es7}J5F-1zfaKpJtC)N5Zq*Iheszxi#( z#hrp7^gL@(V%D;u0!}TjKVz}2{WGScG1BJ|&Auh3&kFEw>hJR_%JyuDSU4Qd;|Jc>;n1 zPi#(tqEW@y&jW_3&c8COBA+@gT6Ekog;~X1 zZWFS*Xq|yeMizh2qjU2}i&8`^E(d}NX9LKTm&~2zmBgv?POU*GLDm%&*OrELQ zTrv94&fSn!Uj9@fSp4ESIw;H%*!B7lu1!Oz@z0%Yp_QvV{O(rvH>B@s_@oF!$eLA3 z^RBATLt{Owcr%KampFcS=^pxq^WG=qN3%c8dtPqsvc#nR()iJrlfeC#k^Y@yz@PYOF$0*doSyfn3g6vpe{I_wH$xb>@RX;R{H zeZ8hUD5X}a#YCB>B04Y{X4zy#OAhldGaM!=62S0N+k2dqMfwK}NjWUYLJ|uQ;_zW6 znbKs7<&n^3e#?RUM0B}ix41P4vQYcYncg|Gn{LRIODUvUMij2xyzgAqi?T(^oT6mi zlH`{u?DAMlM4$1wP(kkwe=p-4jWWKpC1z86-@MG8wTJ09cN)V&E>|v1du*!ZL8kyP zTgypY4`%gdS~zw>x!QB5DEbNk*KC-QdbkHoy5r`wB;szr?^SG}Fc~c^FwS za6q?LTH6~phPNBm9@_f<5ar6*ghJqbX%6R!)bpCO^b@u(&eJHgh;ZaMu5^DsnpI?K zcNhOW*KhdK_wGD1kp_BOGcKS_hrv`0FS0f&)*>%bH&L=G_uend7z9f~eN(s4-JVHv zXeEgxW4ito6;!ew0TU}=*Oei z0U18beEuw}*k?bot7)9>x)J2;5h2LPa4*PL~1`8%HzJ5MhW?6#FV}8;7nVL9CgH}&$ZsIuURivw1pZ- zl^EL%You#SI3YW4Sk7z&K(v~+6PB1tc5@YhSPrxR`@}i+fQS;y{APFLf}~+U;?^4r z8#4N7(5LD!x(~4y>_3Y7hTV6Q50N2pBahfIY$XozU@r97V+^Ree8Qcy|m z1na_=R%06hE&bH8@9)ZsJ9<8qkdr^PIWhTuUM>L1PaXDdMA=&oC2gosLwb_SV%&pT zFSAowSF;DlYv|K&GXl*28y$X7S{T85b_=f5uB?nUE}Yyr^)AhJ+3GL%C~8|~EDjNLHzvV;Y3P86T}h`8Q-SzN$RC?qb9_)|TK7pwuXXh#2={ubrl_D_@jSb{~s+&U:/data --volume=:/code \ + --name=ganslate ganslate:latest /bin/bash +``` + + + +The docker container [mounts volumes from the host system](https://docs.docker.com/storage/volumes/) to allow easier persistence of data. + +`` must be replaced with the full path of a directory where your data is located. It can also point to an empty directory during setup (Data can be moved into this directory later as docker mounts the directory to the container). + +`` must be replaced with the path to the `ganslate` repository. + +## Conda + +The framework can be installed with Conda through following the steps, + +1. Create a [conda environment](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) from the `environment.yaml` file + +```console +conda env create -f environment.yml +``` \ No newline at end of file diff --git a/docs/tutorials/your_first_run.md b/docs/tutorials/your_first_run.md new file mode 100644 index 0000000..380713a --- /dev/null +++ b/docs/tutorials/your_first_run.md @@ -0,0 +1,25 @@ +# Your First Run With horse2zebra Dataset + +**Docker:** + +The horse2zebra dataset can be downloaded to the `` in the host system using instructions below, + +1. Open a terminal inside the cloned repository and run, + +```console +cd projects/horse2zebra +bash download_cyclegan_dataset.sh horse2zebra +``` + +2. Next, the following commands are to be run in the docker container shell + +![docker_commands](../imgs/your_first_run_docker.png) + +Run the training using, + +```console +cd /code +python tools/train.py config=projects/horse2zebra/experiments/default_docker.yaml +``` + +NOTE: If you have more than one GPU, then you can either run the training in distributed mode or set CUDA_VISIBLE_DEVICES environment variable to use only single GPUs. \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..10f48c2 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,9 @@ +site_name: GANslate + +nav: + - Home: index.md + - Installation: installation.md + - Tutorials: + - Your First Run: tutorials/your_first_run.md + +theme: readthedocs \ No newline at end of file