Fets data prep helper

cli/medperf/config.py

@@ -69,7 +69,6 @@
 test_report_file = "test_report.yaml"
 cube_filename = "mlcube.yaml"
 params_filename = "parameters.yaml"
-stages_filename = "stages.yaml"
 additional_path = "workspace/additional_files"
 tarball_filename = "tmp.tar.gz"
 image_path = "workspace/.image"

cli/medperf/decorators.py

@@ -38,8 +38,7 @@ def wrapper(*args, **kwargs):
             config.ui.print(str(e))
         except MedperfException as e:
             logging.exception(e)
-            logs_path = storage_path(config.logs_storage)
-            log_filepath = os.path.join(logs_path, config.log_file)
+            log_filepath = storage_path(config.log_file)
             additional_msg = f"For more information, check the logs at: {log_filepath}"
             msg = ". ".join([str(e), additional_msg])
             pretty_error(msg)

cli/requirements.txt

@@ -1,5 +1,5 @@
 typer~=0.6.0
-rich~=12.5.0
+rich>=12.5.0
 PyYAML>6
 requests>=2.26.0
 pydantic==1.10.2

scripts/assets/brainmask.label

@@ -0,0 +1,21 @@
+################################################
+# ITK-SnAP Label Description File
+# File format: 
+# IDX   -R-  -G-  -B-  -A--  VIS MSH  LABEL
+# Fields: 
+#    IDX:   Zero-based index 
+#    -R-:   Red color component (0..255)
+#    -G-:   Green color component (0..255)
+#    -B-:   Blue color component (0..255)
+#    -A-:   Label transparency (0.00 .. 1.00)
+#    VIS:   Label visibility (0 or 1)
+#    IDX:   Label mesh visibility (0 or 1)
+#  LABEL:   Label description 
+################################################
+    0     0    0    0        0  0  0    "Background"
+    1   255    0    0        1  1  1    "Brain Mask"
+    2     0  255    0        1  1  1    "Label 2"
+    3     0    0  255        1  1  1    "Label 3"
+    4   255  255    0        1  1  1    "Label 4"
+    5     0  255  255        1  1  1    "Label 5"
+    6   255    0  255        1  1  1    "Label 6"

scripts/assets/list_view.tcss

@@ -0,0 +1,13 @@
+Screen {
+    align: center middle;
+}
+
+ListView {
+    width: 30;
+    height: auto;
+    margin: 2 2;
+}
+
+Label {
+    padding: 1 2;
+}

scripts/assets/monitor-dset.tcss

@@ -0,0 +1,152 @@
+Screen {
+    background: $surface-darken-3;
+    align: center middle;
+    layers: base dialog;
+}
+
+#list-container {
+    width: 25%;
+    height: 100%;
+    dock: left;
+    background: $primary-background-darken-1
+}
+
+ListItem {
+    padding: 1;
+}
+
+#subjects-list {
+    height: 100%;
+}
+
+SubjectDetails {
+    display: none;
+    padding: 1 3 1 3;
+    align: center middle;
+    content-align: center middle;
+    align: center middle;
+}
+
+#subject-title {
+    margin: 1;
+    text-style: bold;
+    # background: $primary-background-darken-1;
+}
+
+#subject-title Static {
+    text-align: center;
+    padding: 1;
+}
+
+SubjectDetails #review-buttons {
+    margin: 0 5;
+}
+
+SubjectDetails #review-buttons Static {
+    text-align: center;
+}
+
+.warning {
+    border: tall $warning;
+}
+
+SubjectDetails Button {
+    text-align: center;
+    width: 100%;
+    margin: 1;
+}
+
+#subject-status {
+    color: $accent-lighten-3;
+}
+
+.subject-item-label {
+    text-style: bold;
+    width: auto;
+    color: $panel-lighten-2;
+    column-span: 2;
+}
+
+.subject-item-content {
+    column-span: 8;
+    overflow: scroll;
+}
+
+.subject-item-copy {
+    column-span: 2;
+}
+
+SubjectDetails {
+    overflow-y: scroll;
+    height: 100%;
+}
+
+SubjectDetails CopyableItem {
+    layout: grid;
+    grid-size: 12 1;
+    grid-columns: 1fr;
+    grid-gutter: 1;
+    margin: 1;
+    height: auto;
+}
+
+Button.prompt-btn {
+    margin: 1;
+}
+
+#confirm-prompt {
+    layer: dialog;
+    align: center middle;
+    width: 30%;
+    height: auto;
+    background: $primary-background-lighten-1;
+    content-align: center middle;
+}
+
+#confirm-details {
+    content-align: center middle;
+    padding: 1 0 1 0;
+    height: auto;
+}
+
+#confirm-buttons {
+    padding: 0 1 0 0;
+    height: auto;
+}
+
+#confirm-approve {
+    width: 50%;
+}
+
+#confirm-deny {
+    width: 50%;
+}
+
+Summary {
+    padding: 3;
+    align: center middle;
+    content-align: center middle;
+    overflow-y: scroll;
+}
+
+Summary Static {
+    text-align: center;
+    text-style: bold;
+}
+
+#summary-content {
+    margin: 3 0 1 0;
+}
+
+Center.pbar {
+    height: auto;
+}
+
+ListItem.highlight {
+    background: $secondary-lighten-3;
+}
+
+MarkdownViewer {
+    height: auto;
+    min-height: 2;
+}

scripts/assets/postop_gbm.label

@@ -0,0 +1,21 @@
+################################################
+# ITK-SnAP Label Description File
+# File format: 
+# IDX   -R-  -G-  -B-  -A--  VIS MSH  LABEL
+# Fields: 
+#    IDX:   Zero-based index 
+#    -R-:   Red color component (0..255)
+#    -G-:   Green color component (0..255)
+#    -B-:   Blue color component (0..255)
+#    -A-:   Label transparency (0.00 .. 1.00)
+#    VIS:   Label visibility (0 or 1)
+#    IDX:   Label mesh visibility (0 or 1)
+#  LABEL:   Label description 
+################################################
+    0     0    0    0        0  0  0    "Background"
+    1   255    0    0        1  1  1    "Necrotic Tumor Core"
+    2     0  255    0        1  1  1    "Tumor Infiltration & Edema"
+    3     0    0  255        1  1  1    "Enhancing Tumor Core"
+    4   255  255    0        1  1  1    "Resection Cavity"
+    5     0  255  255        1  1  1    "Label 5"
+    6   255    0  255        1  1  1    "Label 6"