From 2caf9fc98896edbb14b11580cdf03bd33f770f6e Mon Sep 17 00:00:00 2001 From: Suraj Pai Date: Sun, 10 Mar 2024 21:37:02 -0400 Subject: [PATCH] Deployed 70d745f with MkDocs version: 1.5.3 --- 404.html | 1235 +++- assets/_mkdocstrings.css | 109 + getting-started/cloud-quick-start/index.html | 1235 +++- getting-started/installation/index.html | 1235 +++- getting-started/quick-start/index.html | 1235 +++- .../repository-structure/index.html | 1235 +++- index.html | 1237 +++- objects.inv | Bin 0 -> 2066 bytes reference/SUMMARY/index.html | 1386 +++- reference/callbacks/index.html | 2054 ++++++ .../callbacks/prediction_saver/index.html | 2999 +++++++++ reference/callbacks/utils/index.html | 2391 +++++++ reference/datasets/index.html | 2188 +++++++ .../datasets/ssl_radiomics_dataset/index.html | 3424 ++++++++++ reference/datasets/utils/index.html | 2406 +++++++ reference/models/autoencoder/index.html | 2874 +++++++++ reference/models/index.html | 2054 ++++++ reference/models/load_model/index.html | 3126 +++++++++ reference/models/models_genesis/index.html | 5614 +++++++++++++++++ reference/optimizers/index.html | 2054 ++++++ reference/optimizers/lars/index.html | 3193 ++++++++++ reference/preprocessing/index.html | 2054 ++++++ .../preprocessing/seed_based_crop/index.html | 3277 ++++++++++ reference/run/index.html | 2340 +++++++ reference/ssl/index.html | 2054 ++++++ reference/ssl/losses/index.html | 2056 ++++++ .../neg_mining_info_nce_loss/index.html | 3470 ++++++++++ reference/ssl/losses/nnclr_loss/index.html | 2428 +++++++ reference/ssl/losses/ntxent_loss/index.html | 2446 +++++++ .../ssl/losses/ntxent_mined_loss/index.html | 2901 +++++++++ reference/ssl/losses/swav_loss/index.html | 2578 ++++++++ reference/ssl/modules/exneg_simclr/index.html | 2627 ++++++++ reference/ssl/modules/index.html | 2056 ++++++ reference/ssl/modules/nnclr/index.html | 2728 ++++++++ reference/ssl/modules/simclr/index.html | 2618 ++++++++ reference/ssl/modules/swav/index.html | 3532 +++++++++++ reference/transforms/duplicate/index.html | 2463 ++++++++ reference/transforms/index.html | 2054 ++++++ reference/transforms/med3d/index.html | 2521 ++++++++ reference/transforms/multicrop/index.html | 2461 ++++++++ .../transforms/random_resized_crop/index.html | 2474 ++++++++ reference/utils/download_utils/index.html | 2258 +++++++ reference/utils/idc_helper/index.html | 3566 +++++++++++ reference/utils/index.html | 2054 ++++++ reference/visualization/index.html | 2054 ++++++ reference/visualization/verify_io/index.html | 2327 +++++++ search/search_index.json | 2 +- sitemap.xml.gz | Bin 127 -> 127 bytes user-guide/analysis/index.html | 1241 +++- user-guide/data/index.html | 1235 +++- user-guide/download_models/index.html | 1235 +++- user-guide/fm_adaptation/index.html | 1235 +++- user-guide/inference/index.html | 1235 +++- user-guide/reproduce_baselines/index.html | 1235 +++- user-guide/reproduce_fm/index.html | 1235 +++- 55 files changed, 115170 insertions(+), 164 deletions(-) create mode 100644 objects.inv create mode 100644 reference/callbacks/index.html create mode 100644 reference/callbacks/prediction_saver/index.html create mode 100644 reference/callbacks/utils/index.html create mode 100644 reference/datasets/index.html create mode 100644 reference/datasets/ssl_radiomics_dataset/index.html create mode 100644 reference/datasets/utils/index.html create mode 100644 reference/models/autoencoder/index.html create mode 100644 reference/models/index.html create mode 100644 reference/models/load_model/index.html create mode 100644 reference/models/models_genesis/index.html create mode 100644 reference/optimizers/index.html create mode 100644 reference/optimizers/lars/index.html create mode 100644 reference/preprocessing/index.html create mode 100644 reference/preprocessing/seed_based_crop/index.html create mode 100644 reference/run/index.html create mode 100644 reference/ssl/index.html create mode 100644 reference/ssl/losses/index.html create mode 100644 reference/ssl/losses/neg_mining_info_nce_loss/index.html create mode 100644 reference/ssl/losses/nnclr_loss/index.html create mode 100644 reference/ssl/losses/ntxent_loss/index.html create mode 100644 reference/ssl/losses/ntxent_mined_loss/index.html create mode 100644 reference/ssl/losses/swav_loss/index.html create mode 100644 reference/ssl/modules/exneg_simclr/index.html create mode 100644 reference/ssl/modules/index.html create mode 100644 reference/ssl/modules/nnclr/index.html create mode 100644 reference/ssl/modules/simclr/index.html create mode 100644 reference/ssl/modules/swav/index.html create mode 100644 reference/transforms/duplicate/index.html create mode 100644 reference/transforms/index.html create mode 100644 reference/transforms/med3d/index.html create mode 100644 reference/transforms/multicrop/index.html create mode 100644 reference/transforms/random_resized_crop/index.html create mode 100644 reference/utils/download_utils/index.html create mode 100644 reference/utils/idc_helper/index.html create mode 100644 reference/utils/index.html create mode 100644 reference/visualization/index.html create mode 100644 reference/visualization/verify_io/index.html diff --git a/404.html b/404.html index cf2f3f5..575a906 100644 --- a/404.html +++ b/404.html @@ -262,16 +262,26 @@ -
  • - - + + + + + + +
  • + + API Reference - -
  • + + + + + + @@ -623,19 +633,1230 @@ -
  • - + + + + + + + +
  • + + + + + + + + + +
  • + + diff --git a/assets/_mkdocstrings.css b/assets/_mkdocstrings.css index e69de29..4b7d98b 100644 --- a/assets/_mkdocstrings.css +++ b/assets/_mkdocstrings.css @@ -0,0 +1,109 @@ + +/* Avoid breaking parameter names, etc. in table cells. */ +.doc-contents td code { + word-break: normal !important; +} + +/* No line break before first paragraph of descriptions. */ +.doc-md-description, +.doc-md-description>p:first-child { + display: inline; +} + +/* Max width for docstring sections tables. */ +.doc .md-typeset__table, +.doc .md-typeset__table table { + display: table !important; + width: 100%; +} + +.doc .md-typeset__table tr { + display: table-row; +} + +/* Defaults in Spacy table style. */ +.doc-param-default { + float: right; +} + +/* Symbols in Navigation and ToC. */ +:root, +[data-md-color-scheme="default"] { + --doc-symbol-attribute-fg-color: #953800; + --doc-symbol-function-fg-color: #8250df; + --doc-symbol-method-fg-color: #8250df; + --doc-symbol-class-fg-color: #0550ae; + --doc-symbol-module-fg-color: #5cad0f; + + --doc-symbol-attribute-bg-color: #9538001a; + --doc-symbol-function-bg-color: #8250df1a; + --doc-symbol-method-bg-color: #8250df1a; + --doc-symbol-class-bg-color: #0550ae1a; + --doc-symbol-module-bg-color: #5cad0f1a; +} + +[data-md-color-scheme="slate"] { + --doc-symbol-attribute-fg-color: #ffa657; + --doc-symbol-function-fg-color: #d2a8ff; + --doc-symbol-method-fg-color: #d2a8ff; + --doc-symbol-class-fg-color: #79c0ff; + --doc-symbol-module-fg-color: #baff79; + + --doc-symbol-attribute-bg-color: #ffa6571a; + --doc-symbol-function-bg-color: #d2a8ff1a; + --doc-symbol-method-bg-color: #d2a8ff1a; + --doc-symbol-class-bg-color: #79c0ff1a; + --doc-symbol-module-bg-color: #baff791a; +} + +code.doc-symbol { + border-radius: .1rem; + font-size: .85em; + padding: 0 .3em; + font-weight: bold; +} + +code.doc-symbol-attribute { + color: var(--doc-symbol-attribute-fg-color); + background-color: var(--doc-symbol-attribute-bg-color); +} + +code.doc-symbol-attribute::after { + content: "attr"; +} + +code.doc-symbol-function { + color: var(--doc-symbol-function-fg-color); + background-color: var(--doc-symbol-function-bg-color); +} + +code.doc-symbol-function::after { + content: "func"; +} + +code.doc-symbol-method { + color: var(--doc-symbol-method-fg-color); + background-color: var(--doc-symbol-method-bg-color); +} + +code.doc-symbol-method::after { + content: "meth"; +} + +code.doc-symbol-class { + color: var(--doc-symbol-class-fg-color); + background-color: var(--doc-symbol-class-bg-color); +} + +code.doc-symbol-class::after { + content: "class"; +} + +code.doc-symbol-module { + color: var(--doc-symbol-module-fg-color); + background-color: var(--doc-symbol-module-bg-color); +} + +code.doc-symbol-module::after { + content: "mod"; +} \ No newline at end of file diff --git a/getting-started/cloud-quick-start/index.html b/getting-started/cloud-quick-start/index.html index 742a191..7b2451c 100644 --- a/getting-started/cloud-quick-start/index.html +++ b/getting-started/cloud-quick-start/index.html @@ -273,16 +273,26 @@ -
  • - - + + + + + + +
  • + + API Reference - -
  • + + + + + + @@ -649,19 +659,1230 @@ -
  • - + + + + + + + +
  • + + + + + + + + + +
  • + + diff --git a/getting-started/installation/index.html b/getting-started/installation/index.html index a49c14b..3957e90 100644 --- a/getting-started/installation/index.html +++ b/getting-started/installation/index.html @@ -273,16 +273,26 @@ -
  • - - + + + + + + +
  • + + API Reference - -
  • + + + + + + @@ -712,19 +722,1230 @@ -
  • - + + + + + + + +
  • + + + + + + + + + +
  • + + diff --git a/getting-started/quick-start/index.html b/getting-started/quick-start/index.html index 761f0d7..2e53592 100644 --- a/getting-started/quick-start/index.html +++ b/getting-started/quick-start/index.html @@ -273,16 +273,26 @@ -
  • - - + + + + + + +
  • + + API Reference - -
  • + + + + + + @@ -721,19 +731,1230 @@ -
  • - + + + + + + + +
  • + + + + + + + + + +
  • + + diff --git a/getting-started/repository-structure/index.html b/getting-started/repository-structure/index.html index a42e86a..824c6a7 100644 --- a/getting-started/repository-structure/index.html +++ b/getting-started/repository-structure/index.html @@ -267,16 +267,26 @@ -
  • - - + + + + + + +
  • + + API Reference - -
  • + + + + + + @@ -628,19 +638,1230 @@ -
  • - + + + + + + + +
  • + + + + + + + + + +
  • + + diff --git a/index.html b/index.html index ecde5a2..52399e2 100644 --- a/index.html +++ b/index.html @@ -271,16 +271,26 @@ -
  • - - + + + + + + +
  • + + API Reference - -
  • + + + + + + @@ -719,19 +729,1230 @@ -
  • - + + + + + + + +
  • + + + + + + + + + +
  • + + @@ -839,7 +2060,7 @@

    Documentation Walkthrough

    Replication Guide
    If you would like to pre-train a foundation model on your own unannotated data or would like to replicate the training and evaluation from our study, see here.

    Tutorials
    We provide comprehensive tutorials that use the foundation model for cancer imaging biomarkers and compare against other popularly used methods. If you would like to build your own study using our foundation model, these set of tutorials are highly recommended as the starting point.

    -

    API Docs
    This is for the more advanced user who would like to deep-dive into different methods and classes provided by our package.

    +

    API Docs
    This is for the more advanced user who would like to deep-dive into different methods and classes provided by our package.

    License

    This project is licensed under the terms of the MIT license. See LICENSE for more details.

    diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000000000000000000000000000000000000..48fef81e1586d9007ac3156169b750910a7cd1a6 GIT binary patch literal 2066 zcmV+t2<`VHAX9K?X>NERX>N99Zgg*Qc_4OWa&u{KZXhxWBOp+6Z)#;@bUGkLZ*^{D zVRUJ4ZXiu>WMyn1W^ZyJLt$=XWpW@%ZDD6=Zf77uX>V;|a%*LBa|$CMR%LQ?X>V>i zATTa4E-(rsAXI2&AaZ4GVQFq;WpW^IW*~HEX>%ZEX>4U6X>%ZBZ*6dLWpi_7WFU2O zX>MmAdTeQ8E(&DB8x4@Ph#+i6AtuAW0f?e)iGGC=OK-mo3@*w?p8t#*xBt48tbgo*YN9 z3BcO>x~58m5Xp%^NXhNWyt=xsqPmJ?tw#b+h-C2|PN)6EhyWyup`ghjUl0F z8jF7S%oDd1B<07mwYsc<0#xtg9H(ILb%Jn@b*x=g@~(zPVPgYWe3}Tec0Z7ZV-a%@ zwr;h>rY6yLdwm;YLNk)^%le`@VI3%(r--#pP;^f z6!O;+m(HU!zJoexy^ekk`&baU0rEI2Qh2>UWHLB`4Gijj)(II2ig*zxB;Q-Nrh{~E zXFAB#S>BEfjEkov@okbpk?5c!ZPx}lq;D+EBf=4t8+#fT#n87&ys#megtoaF29qX% z)vmhmxO#M63VM|%@;}VH*)}a>Sr6)Z?NBxZtt7fAxuDtk)llV{#`v51)2WflTB!Pa zAkh_Qq=7_rk$;g}Ehqff4Tw*dPODn>?vk=d9b=Ti`rl7?(rEW4G%23pt<-Qi{$=>vg{Lf zj@C?egpzwm9^?QPrCg9C^O-VNFK|T1%3R7-^;6y`aZ(YNbgYjKp6oMaR`TikmmHAC zMg6IftNGI4SMuX~DdfaoY32;!t9f)Jw31uH1JYv1)tqVYYxz;EG;?(DdfpW4&lr@& z4}kJE=}be@LXeF70cP80y9(xJ(e?T5)_ktlnx-*3oYl0p>T(S*fK{PCsG7X70S4jC zfcWRic%Zs(6zX@#<)BGP@|VeeEsl*l&ibm_APm5f^Es0J;Ax_A`QCJb%}%RC2HlarH6Jrrkn~Uq)YsxLp?zQ%Lo}>(^|Fjlpn66MGn&f`|3%Ll>6VI}$Rj@17p;pP8=7;@n zBnLc3KT{1nQFL{zYNo)tN^(Mf&3E+X;_5;@0cX8aqAfnyD`DAGE}R`jve+7?rK&Fk zL(to&_;-+f{3(94#d9d@a0V$`)c&b%w`Ma&D0qZkH4J~^e2tJ)uKue+^4+$aJ|bCo z4-7$e2N=r={4a`4?zIWcic%it3(8T2iTT4C5gvAqfOV~HK^~ZCV_T9sZq-dv7&BwN z0^N2QV6(pS`f$cAePQr8v!{xT@jFzbI~fGqt{*tU(EcONsT8LS)Pm~cN6;&NII8%^ zPdo9rQHDd*V#rY=FabZpVk^D2(dB4U!_qLidX{6qC7H~W_H$^NMagxatsh>q# zm|or^o0O~U?ANUFu}Q2dXecIrXs7JmX*%NQgBr^K1vz>~zPw%|Ol;lEfbs2*&Blu~ zkNg_+uywSEQpl1TBUH_?0P~wk>VOQV`&`mEQ-i5v40J++=dF7H`b*I3-U!$@1IK{J zcQvI;^UkRo9Sb_>FUJBq#@_BhTYEXixbBIDc1C)Tw zwsUtC%*~?9vPenNd`fV<{b=oRTeIDQG|Hh&;~B)h<^t3+%NO-NNt}{D@I8m$G%Yi~ zdllUX7_3#bZ#&5JSk%i*jsq<8dqXuaW_3$C|sJp(d zIQqDte#LoP7KM7f`3GyhT|3^k>Xrm2=pNFd`&gj)7~^n#!0PLq@CEIrs3a+FzUZhP zT&s^lJ<0)nG-LbHILSEdKjwtY*V9-7k=BXpUpHSqEFje9S;TJ7FTZ|YP^{)z#CA;1 z^(@ZG4!BrQw9mDO``6NNo^G5d`wAFO?mFcRQ1`@+u%&=ycrv|#JQ}zjOwNNpJ9FnK zwm)S|Mq5(Cbe?_n&u1Pl^7%~rTAs{q-b|81#RzaYSZoH@1Dlj^49r&ak?>NTlH>O6 wWWyrv)zKsF6-1AczI#E024N1h1AvF?5b}NdcpV@8V+egh58l1`AL-w($^