more renaming, doc adjustments etc.

Tomographer · Jul 5, 2018 · a4d08be · a4d08be
1 parent 071ec04
commit a4d08be
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Showing 6 changed files with 91 additions and 36 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -21,7 +21,7 @@ message(WARNING "
   
     > python setup.py install
   
-  Check out the README file for more information.
+  Check out the README.md file for more information.
   ============================================================================
 ")
 
@@ -33,7 +33,7 @@ find_package(Boost COMPONENTS unit_test_framework REQUIRED)
 
 find_package(Threads REQUIRED)
 
-find_package(TomographerPy 5.3 REQUIRED)
+find_package(TomographerPy 5.4 REQUIRED)
 
 
 include_directories(${SCS_INCLUDE_DIRS})

diff --git a/QPtomographer/util.py b/QPtomographer/util.py
@@ -171,8 +171,8 @@ def simulate_process_prep_measure(E_AB, prep_meas_settings):
     `num_repeats` is the number of times to repeat this setting.
 
     Returns: an object `d` with properties `d.Emn_ch`, `d.Nm`, representing the
-    arguments suitable for `QPtomographer.channelspace.run()` and the simulated
-    frequency counts.
+    arguments suitable for :py:meth:`QPtomographer.channelspace.run()` and the
+    simulated frequency counts.
     """
 
     Emn_ch = []

diff --git a/cxx/channelspace.h b/cxx/channelspace.h
@@ -36,18 +36,18 @@ struct ChannelTypes : public Tomographer::DenseDM::DMTypes<Eigen::Dynamic,Scalar
   typedef Eigen::Matrix<ComplexScalar, Eigen::Dynamic, Eigen::Dynamic, Eigen::ColMajor> VIsometryType;
 
 private:
-  std::size_t dim_x;
-  std::size_t dim_y;
+  Eigen::Index dim_x;
+  Eigen::Index dim_y;
 
 public:
-  ChannelTypes(std::size_t dim_x_, std::size_t dim_y_)
+  ChannelTypes(Eigen::Index dim_x_, Eigen::Index dim_y_)
     : Base(dim_x_*dim_y_), dim_x(dim_x_), dim_y(dim_y_)
   {
   }
 
-  inline std::size_t dimX() const { return dim_x; }
-  inline std::size_t dimY() const { return dim_y; }
-  inline std::size_t dimXY2() const { return Base::dim()*dim_y; }
+  inline Eigen::Index dimX() const { return dim_x; }
+  inline Eigen::Index dimY() const { return dim_y; }
+  inline Eigen::Index dimXY2() const { return Base::dim()*dim_y; }
 
 };
 

diff --git a/cxx/worstentglfidelity_figofmerit.h b/cxx/worstentglfidelity_figofmerit.h
@@ -289,7 +289,7 @@ class WorstEntglFidelitySCSSolver
     const scs_int dvmu = 1;
     const scs_int dvzRdiag = DimX;
     const scs_int dvzRtri = DimX*(DimX-1)/2;
-    const scs_int dvzItri = dvzRtri; // == DimX*(DimX-1)/2;
+    //const scs_int dvzItri = dvzRtri; // == DimX*(DimX-1)/2;
 
     const scs_int var_mu_offset = 0;
     const scs_int var_zRdiag_offset = var_mu_offset + dvmu;
@@ -333,7 +333,7 @@ class WorstEntglFidelitySCSSolver
     //   **  number of columns = 1 + DimX*DimX = # of variable degrees of freedom
     //       == 1 + dzR + dzI  (dzR = DimX*(DimX+1)/2 , dzI = DimX*(DimX-1)/2)
 
-    scs_int i, j, ip, jp, ij, k;
+    scs_int i, ip, jp, ij, k;
     scs_int trivarno;
 
     logger.longdebug([&](std::ostream & stream) {
@@ -573,8 +573,8 @@ class WorstEntglFidelitySCSSolver
 
     std::vector<std::vector<std::string> > fmtall;
     fmtall.resize(Amat.rows());
-    int w = 0;
-    int i, j;
+    std::size_t w = 0;
+    Eigen::Index i, j;
     for (i = 0; i < Amat.rows(); ++i) {
       fmtall[i].resize(Amat.cols());
       for (j = 0; j < Amat.cols(); ++j) {
@@ -592,7 +592,9 @@ class WorstEntglFidelitySCSSolver
     fmtall.insert(fmtall.begin(), std::vector<std::string>());
     fmtall[0].resize(1+DimX*DimX);
     fmtall[0][0] = "mu  ";
-    for (i = 0; i < DimX; ++i) { fmtall[0][1+i] = "rhoR("+std::to_string(i)+","+std::to_string(i)+")  "; }
+    for (i = 0; i < DimX; ++i) {
+      fmtall[0][1+i] = "rhoR("+std::to_string(i)+","+std::to_string(i)+")  ";
+    }
     int varcount = 0;
     for (j = 0; j < DimX; ++j) {
       for (i = j+1; i < DimX; ++i) {
@@ -603,9 +605,9 @@ class WorstEntglFidelitySCSSolver
 
     std::vector<std::string> lines;
     lines.resize(fmtall.size());
-    for (i = 0; i < fmtall.size(); ++i) {
+    for (i = 0; i < (Eigen::Index)fmtall.size(); ++i) {
       lines[i] = std::string();
-      for (j = 0; j < fmtall[i].size(); ++j) {
+      for (j = 0; j < (Eigen::Index)fmtall[i].size(); ++j) {
         lines[i] += std::string(w - fmtall[i][j].size(), ' ') + fmtall[i][j];
       }
     }
@@ -616,13 +618,13 @@ class WorstEntglFidelitySCSSolver
     const scs_int dC1 = 2*DimX;
     const scs_int dC2 = 2*(1+DimXX);
     // # of degrees of freedom of each constraint block (== number of corresponding rows in A)
-    const scs_int dC0x = 1;
-    const scs_int dC1x = dC1*(dC1+1)/2;
-    const scs_int dC2x = dC2*(dC2+1)/2;
+    //const scs_int dC0x = 1;
+    //const scs_int dC1x = dC1*(dC1+1)/2;
+    //const scs_int dC2x = dC2*(dC2+1)/2;
     // offset for each constraint number
-    const scs_int con_offset_0 = 0;
-    const scs_int con_offset_1 = con_offset_0+dC0x;
-    const scs_int con_offset_2 = con_offset_1+dC1x;
+    //const scs_int con_offset_0 = 0;
+    //const scs_int con_offset_1 = con_offset_0+dC0x;
+    //const scs_int con_offset_2 = con_offset_1+dC1x;
 
     // the labels come first
 

diff --git a/doc/_static/custom.css b/doc/_static/custom.css
@@ -1,33 +1,68 @@
 
-@import url('https://fonts.googleapis.com/css?family=Source+Sans+Pro:400,400i,600,600i');
+@import url('https://fonts.googleapis.com/css?family=PT+Serif:400,400i,700,700i|Roboto:300,400,400i,500');
 
 body {
     font-weight: 400;
 }
 
+a, a:hover {
+    text-decoration: none;
+}
 
 .logo {
     padding-bottom: 0.75em;
 }
 div.sphinxsidebar .logo a {
     border-bottom: none 0px;
 }
+.sphinxsidebar .toctree-l1 {
+    padding-bottom: 0.5em;
+    list-style: disc;
+}
+div.sphinxsidebarwrapper .caption-text {
+    display: none;
+}
 
 div.body h1 {
     margin-bottom: 0.5em;
 }
 div.body h2 {
     margin-bottom: 0.5em;
 }
+#indices-and-tables {
+    margin-top: 2.5em;
+}
 
 pre {
-    background-color: inherit;
     border-left: solid 1em rgba(0,0,80,0.1);
     padding: 5px 1.5em;
 }
 dl pre, blockquote pre, li pre {
     padding-left: 1.3em;
 }
+pre, tt, code {
+    font-weight: 400;
+}
+code.xref, a code {
+    font-weight: 500;
+    /*color: rgba(0, 65, 114, 1.0);*/
+    border-bottom: 1px dotted #004B6B;
+}
+tt.descname, code.descname {
+    padding: 0px;
+    font-weight: 500;
+}
+tt.descclassname, code.descclassname {
+    padding: 0px;
+    font-weight: 300;
+}
+
+pre, tt, code {
+    background-color: rgba(0,0,80,0.06);
+}
+tt, code {
+    padding: 1px 2px;
+}
 
 
 div.section > dl > dt {
@@ -36,17 +71,35 @@ div.section > dl > dt {
     border-top: solid 0.25em rgba(0,40,70,0.5);
 }
 
+div.important {
+    background-color: rgba(255,207,0,0.15);
+    border: 1px solid rgba(255,207,0,0.5);
+}
 
 
-.sphinxsidebar .toctree-l1 {
-    padding-bottom: 0.5em;
-    list-style: disc;
+div.genindex-jumpbox {
+    font-family: "Roboto", sans-serif;
+    font-weight: 500;
+    border: solid 0.5px rgba(62, 67, 73, 0.4);
 }
-
-.genindextable {
-    font-size: 0.8em;
+div.genindex-jumpbox a {
+    text-decoration: none;
+    display: inline-block;
+    padding: 2px;
+}
+div.body .genindextable {
+    font-size: 0.9em;
+}
+#index ~ h2 {
+    font-size: 1.3em;
+    font-weight: 500;
+    margin: 0.5em 0px 0px;
+    border-bottom: solid 0.5px rgba(62, 67, 73, 0.4);
+}
+.genindextable ul {
+    text-indent: -1.2em;
+    margin-left: 1.2em;
 }
-
 
 /* @media screen and (max-width: 870px) { */
 .docutils.field-list > tbody > tr > th.field-name {

diff --git a/doc/conf.py b/doc/conf.py
@@ -49,7 +49,7 @@
 
 # General information about the project.
 project = 'Practical and reliable process tomography'
-copyright = '2017, Philippe Faist'
+copyright = '2018, Philippe Faist'
 author = 'Philippe Faist'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -100,10 +100,10 @@
 # documentation.
 #
 html_theme_options = {
-    'font_family': '"Source Sans Pro", sans-serif',
+    'font_family': '"PT Serif", sans-serif',
     'font_size': '16px',
-    'head_font_family': '"Source Sans Pro", sans-serif',
-    'code_font_family': '"Source Sans Pro", monospace',
+    'head_font_family': '"Roboto", sans-serif',
+    'code_font_family': '"Roboto", monospace',
     'code_font_size': '0.9em',
 }