{"action":"created","comment":{"url":"https://api.github.com/repos/OpenChemistry/tomviz/pulls/comments/64239856","id":64239856,"diff_hunk":"@@ -384,8 +385,175 @@ void PythonGeneratedDatasetReaction::addDataset()\n         shapeLayout->getShape(shape);\n         this->dataSourceAdded(generator.createDataSource(shape));\n       }\n-    }\n     \n+  }\n+  else if (this->Internals->scriptLabel == \"Electron Beam Shape\")\n+  {\n+    QDialog dialog;\n+    dialog.setWindowTitle(\"Generate Electron Beam Shape\");\n+    QVBoxLayout* layout = new QVBoxLayout; //overall layout\n+    //Guide\n+    QLabel *guide = new QLabel;\n+    guide->setText(\"Generate a convergent electron beam in 3D. This represents the 3D probe used for atomic resolution imaging in a scanning transmission electron microscope.\");\n+    guide->setWordWrap(true);\n+    layout->addWidget(guide);\n+    \n+    //Parameter Layout\n+    QGridLayout *parametersLayout = new QGridLayout;\n+    \n+    QLabel *label = new QLabel(\"Beam energy (keV): \", &dialog);\n+    parametersLayout->addWidget(label,0,0,1,2);\n+    QDoubleSpinBox *voltage = new QDoubleSpinBox(&dialog);\n+    voltage->setRange(1,1000000);\n+    voltage->setValue(300);\n+    voltage->setSingleStep(50);\n+    parametersLayout->addWidget(voltage,0,2,1,1);\n+\n+    label = new QLabel(\"Semi-convergence angle (mrad): \", &dialog);\n+    parametersLayout->addWidget(label,1,0,1,2);\n+    QDoubleSpinBox *alpha_max = new QDoubleSpinBox(&dialog);\n+    alpha_max->setRange(0, 500);\n+    alpha_max->setValue(30);\n+    alpha_max->setSingleStep(0.5);\n+    parametersLayout->addWidget(alpha_max,1,2,1,1);\n+ \n+    label = new QLabel(\"Transerve plane (x-y): \", &dialog);\n+    parametersLayout->addWidget(label,2,0,1,1);\n+    label = new QLabel(\"Number of pixels: \", &dialog);\n+    parametersLayout->addWidget(label,2,1,1,1);\n+    QSpinBox *Nxy = new QSpinBox(&dialog);\n+    Nxy->setRange(64, 2048);\n+    Nxy->setValue(256);\n+    Nxy->setSingleStep(1);\n+    parametersLayout->addWidget(Nxy,2,2,1,1);\n+    \n+    label = new QLabel(\"x-y pixel size (angstrom): \", &dialog);\n+    parametersLayout->addWidget(label,3,1,1,1);\n+    QDoubleSpinBox *dxy = new QDoubleSpinBox(&dialog);\n+    dxy->setRange(0, 100);\n+    dxy->setValue(0.1);\n+    dxy->setSingleStep(0.1);\n+    parametersLayout->addWidget(dxy,3,2,1,1);\n+\n+    label = new QLabel(\"Propagation direction (z): \", &dialog);\n+    parametersLayout->addWidget(label,4,0,1,1);\n+    label = new QLabel(\"Number of pixels: \", &dialog);\n+    parametersLayout->addWidget(label,4,1,1,1);\n+    QSpinBox *Nz = new QSpinBox(&dialog);\n+    Nz->setRange(1, 2048);\n+    Nz->setValue(512);\n+    Nz->setSingleStep(1);\n+    parametersLayout->addWidget(Nz,4,2,1,1);\n+    \n+    label = new QLabel(\"Minimum defocus (nm): \", &dialog);\n+    parametersLayout->addWidget(label,5,1,1,1);\n+    QDoubleSpinBox *df_min = new QDoubleSpinBox(&dialog);\n+    df_min->setRange(-1000000,1000000);\n+    df_min->setValue(-50.0);\n+    df_min->setSingleStep(5.0);\n+    parametersLayout->addWidget(df_min,5,2,1,1);\n+    \n+    label = new QLabel(\"Maximum defocus (nm): \", &dialog);\n+    parametersLayout->addWidget(label,6,1,1,1);\n+    QDoubleSpinBox *df_max = new QDoubleSpinBox(&dialog);\n+    df_max->setRange(-1000000,1000000);\n+    df_max->setValue(100.0);\n+    df_max->setSingleStep(5.0);\n+    parametersLayout->addWidget(df_max,6,2,1,1);\n+    \n+    \n+    label = new QLabel(\"Third-order spherical aberration (mm): \", &dialog);\n+    parametersLayout->addWidget(label,0,3,1,2);\n+    QDoubleSpinBox *c3 = new QDoubleSpinBox(&dialog);\n+    c3->setRange(-1000000,1000000);\n+    c3->setValue(0.2);\n+    c3->setSingleStep(0.1);\n+    parametersLayout->addWidget(c3,0,5,1,1);\n+    \n+    label = new QLabel(\"Twofold astigmatism: \", &dialog);\n+    parametersLayout->addWidget(label,1,3,1,1);\n+    label = new QLabel(\"Value (nm): \", &dialog);\n+    parametersLayout->addWidget(label,1,4,1,1);\n+    QDoubleSpinBox *f_a2 = new QDoubleSpinBox(&dialog);\n+    f_a2->setRange(-1000000,1000000);\n+    f_a2->setValue(0.0);\n+    f_a2->setSingleStep(1000);\n+    parametersLayout->addWidget(f_a2,1,5,1,1);\n+    label = new QLabel(\"Orientation (rad): \", &dialog);\n+    parametersLayout->addWidget(label,2,4,1,1);\n+    QDoubleSpinBox *phi_a2 = new QDoubleSpinBox(&dialog);\n+    phi_a2->setValue(0.0);\n+    phi_a2->setSingleStep(0.1);\n+    parametersLayout->addWidget(phi_a2,2,5,1,1);\n+    \n+    label = new QLabel(\"Threefold astigmatism: \", &dialog);\n+    parametersLayout->addWidget(label,3,3,1,1);\n+    label = new QLabel(\"Value (nm): \", &dialog);\n+    parametersLayout->addWidget(label,3,4,1,1);\n+    QDoubleSpinBox *f_a3 = new QDoubleSpinBox(&dialog);\n+    f_a3->setRange(-1000000,1000000);\n+    f_a3->setValue(0.0);\n+    f_a3->setSingleStep(1000);\n+    parametersLayout->addWidget(f_a3,3,5,1,1);\n+    label = new QLabel(\"Orientation (rad): \", &dialog);\n+    parametersLayout->addWidget(label,4,4,1,1);\n+    QDoubleSpinBox *phi_a3 = new QDoubleSpinBox(&dialog);\n+    phi_a3->setValue(0.0);\n+    phi_a3->setSingleStep(0.1);\n+    parametersLayout->addWidget(phi_a3,4,5,1,1);\n+    \n+    label = new QLabel(\"Coma: \", &dialog);\n+    parametersLayout->addWidget(label,5,3,1,1);\n+    label = new QLabel(\"Value (nm): \", &dialog);\n+    parametersLayout->addWidget(label,5,4,1,1);\n+    QDoubleSpinBox *f_c3 = new QDoubleSpinBox(&dialog);\n+    f_c3->setRange(-1000000,1000000);\n+    f_c3->setValue(1500.0);\n+    f_c3->setSingleStep(1000);\n+    parametersLayout->addWidget(f_c3,5,5,1,1);\n+    label = new QLabel(\"Orientation (rad): \", &dialog);\n+    parametersLayout->addWidget(label,6,4,1,1);\n+    QDoubleSpinBox *phi_c3 = new QDoubleSpinBox(&dialog);\n+    phi_c3->setValue(0.0);\n+    phi_c3->setSingleStep(0.1);\n+    parametersLayout->addWidget(phi_c3,6,5,1,1);\n+    \n+    //Buttons\n+    QDialogButtonBox* buttons = new QDialogButtonBox(\n+                                                     QDialogButtonBox::Cancel|QDialogButtonBox::Ok, Qt::Horizontal, &dialog);\n+    QObject::connect(buttons, SIGNAL(accepted()), &dialog, SLOT(accept()));\n+    QObject::connect(buttons, SIGNAL(rejected()), &dialog, SLOT(reject()));\n+    \n+    layout->addItem(parametersLayout);\n+    layout->addWidget(buttons);\n+    dialog.setLayout(layout);\n+    dialog.layout()->setSizeConstraint(QLayout::SetFixedSize); //Make the UI non-resizeable\n+    \n+    // substitute values\n+    if (dialog.exec() == QDialog::Accepted)\n+    {\n+      QString pythonScript = this->Internals->scriptSource;\n+      pythonScript.replace(\"###voltage###\", QString(\"voltage = %1\").arg(voltage->value()));\n+      pythonScript.replace(\"###alpha_max###\", QString(\"alpha_max = %1\").arg(alpha_max->value()));\n+      pythonScript.replace(\"###Nxy###\", QString(\"Nxy = %1\").arg(Nxy->value()));\n+      pythonScript.replace(\"###Nz###\", QString(\"Nz = %1\").arg(Nz->value()));\n+      pythonScript.replace(\"###dxy###\", QString(\"dxy = %1\").arg(dxy->value()));\n+      pythonScript.replace(\"###df_min###\", QString(\"df_min = %1\").arg(df_min->value()));\n+      pythonScript.replace(\"###df_max###\", QString(\"df_max = %1\").arg(df_max->value()));\n+      pythonScript.replace(\"###c3###\", QString(\"c3 = %1\").arg(c3->value()));\n+      pythonScript.replace(\"###f_a2###\", QString(\"f_a2 = %1\").arg(f_a2->value()));\n+      pythonScript.replace(\"###phi_a2###\", QString(\"phi_a2 = %1\").arg(phi_a2->value()));\n+      pythonScript.replace(\"###f_a3###\", QString(\"f_a3 = %1\").arg(f_a3->value()));\n+      pythonScript.replace(\"###phi_a3###\", QString(\"phi_a3 = %1\").arg(phi_a3->value()));\n+      pythonScript.replace(\"###f_c3###\", QString(\"f_c3 = %1\").arg(f_c3->value()));\n+      pythonScript.replace(\"###phi_c3###\", QString(\"phi_c3 = %1\").arg(phi_c3->value()));\n+      generator.setScript(pythonScript);\n+      const int shape[3] = {Nxy->value(),Nxy->value(),Nz->value()};\n+      this->dataSourceAdded(generator.createDataSource(shape));\n+    }\n+  \n+    } //end of else if","path":"tomviz/PythonGeneratedDatasetReaction.cxx","position":185,"original_position":185,"commit_id":"2c75d02a00fc1fd4529a006fb1e4e9c63e72a2dc","original_commit_id":"2c75d02a00fc1fd4529a006fb1e4e9c63e72a2dc","user":{"login":"mathturtle","id":553788,"avatar_url":"https://avatars.githubusercontent.com/u/553788?v=3","gravatar_id":"","url":"https://api.github.com/users/mathturtle","html_url":"https://github.com/mathturtle","followers_url":"https://api.github.com/users/mathturtle/followers","following_url":"https://api.github.com/users/mathturtle/following{/other_user}","gists_url":"https://api.github.com/users/mathturtle/gists{/gist_id}","starred_url":"https://api.github.com/users/mathturtle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mathturtle/subscriptions","organizations_url":"https://api.github.com/users/mathturtle/orgs","repos_url":"https://api.github.com/users/mathturtle/repos","events_url":"https://api.github.com/users/mathturtle/events{/privacy}","received_events_url":"https://api.github.com/users/mathturtle/received_events","type":"User","site_admin":false},"body":"This should be indented only 2 spaces like the opening of this block.  I can fix the indentation stuff though.","created_at":"2016-05-23T15:21:36Z","updated_at":"2016-05-23T15:21:36Z","html_url":"https://github.com/OpenChemistry/tomviz/pull/404#discussion_r64239856","pull_request_url":"https://api.github.com/repos/OpenChemistry/tomviz/pulls/404","_links":{"self":{"href":"https://api.github.com/repos/OpenChemistry/tomviz/pulls/comments/64239856"},"html":{"href":"https://github.com/OpenChemistry/tomviz/pull/404#discussion_r64239856"},"pull_request":{"href":"https://api.github.com/repos/OpenChemistry/tomviz/pulls/404"}}},"pull_request":{"url":"https://api.github.com/repos/OpenChemistry/tomviz/pulls/404","id":70920642,"html_url":"https://github.com/OpenChemistry/tomviz/pull/404","diff_url":"https://github.com/OpenChemistry/tomviz/pull/404.diff","patch_url":"https://github.com/OpenChemistry/tomviz/pull/404.patch","issue_url":"https://api.github.com/repos/OpenChemistry/tomviz/issues/404","number":404,"state":"open","locked":false,"title":"Added a sample data that simulates electron beam shape","user":{"login":"yijiang1","id":13088588,"avatar_url":"https://avatars.githubusercontent.com/u/13088588?v=3","gravatar_id":"","url":"https://api.github.com/users/yijiang1","html_url":"https://github.com/yijiang1","followers_url":"https://api.github.com/users/yijiang1/followers","following_url":"https://api.github.com/users/yijiang1/following{/other_user}","gists_url":"https://api.github.com/users/yijiang1/gists{/gist_id}","starred_url":"https://api.github.com/users/yijiang1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yijiang1/subscriptions","organizations_url":"https://api.github.com/users/yijiang1/orgs","repos_url":"https://api.github.com/users/yijiang1/repos","events_url":"https://api.github.com/users/yijiang1/events{/privacy}","received_events_url":"https://api.github.com/users/yijiang1/received_events","type":"User","site_admin":false},"body":"Added a sample data that simulates electron beam shape.\r\nThe default parameters generate a typical electron beam shape.","created_at":"2016-05-20T21:35:44Z","updated_at":"2016-05-23T15:21:36Z","closed_at":null,"merged_at":null,"merge_commit_sha":"2f9b121682bb28ce44eb621eca4c931f242e41b4","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/OpenChemistry/tomviz/pulls/404/commits","review_comments_url":"https://api.github.com/repos/OpenChemistry/tomviz/pulls/404/comments","review_comment_url":"https://api.github.com/repos/OpenChemistry/tomviz/pulls/comments{/number}","comments_url":"https://api.github.com/repos/OpenChemistry/tomviz/issues/404/comments","statuses_url":"https://api.github.com/repos/OpenChemistry/tomviz/statuses/2c75d02a00fc1fd4529a006fb1e4e9c63e72a2dc","head":{"label":"yijiang1:sample-data-electron-beam","ref":"sample-data-electron-beam","sha":"2c75d02a00fc1fd4529a006fb1e4e9c63e72a2dc","user":{"login":"yijiang1","id":13088588,"avatar_url":"https://avatars.githubusercontent.com/u/13088588?v=3","gravatar_id":"","url":"https://api.github.com/users/yijiang1","html_url":"https://github.com/yijiang1","followers_url":"https://api.github.com/users/yijiang1/followers","following_url":"https://api.github.com/users/yijiang1/following{/other_user}","gists_url":"https://api.github.com/users/yijiang1/gists{/gist_id}","starred_url":"https://api.github.com/users/yijiang1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yijiang1/subscriptions","organizations_url":"https://api.github.com/users/yijiang1/orgs","repos_url":"https://api.github.com/users/yijiang1/repos","events_url":"https://api.github.com/users/yijiang1/events{/privacy}","received_events_url":"https://api.github.com/users/yijiang1/received_events","type":"User","site_admin":false},"repo":{"id":38206349,"name":"tomviz","full_name":"yijiang1/tomviz","owner":{"login":"yijiang1","id":13088588,"avatar_url":"https://avatars.githubusercontent.com/u/13088588?v=3","gravatar_id":"","url":"https://api.github.com/users/yijiang1","html_url":"https://github.com/yijiang1","followers_url":"https://api.github.com/users/yijiang1/followers","following_url":"https://api.github.com/users/yijiang1/following{/other_user}","gists_url":"https://api.github.com/users/yijiang1/gists{/gist_id}","starred_url":"https://api.github.com/users/yijiang1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yijiang1/subscriptions","organizations_url":"https://api.github.com/users/yijiang1/orgs","repos_url":"https://api.github.com/users/yijiang1/repos","events_url":"https://api.github.com/users/yijiang1/events{/privacy}","received_events_url":"https://api.github.com/users/yijiang1/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/yijiang1/tomviz","description":"Cross 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