Dynamic labels with regex

docs/figure_file_format.rst

@@ -36,7 +36,7 @@ This is an example of a minimal OMERO.figure JSON file::
 
     {
     // see older versions below
-    "version": 5,
+    "version": 6,
     "panels": [
         {
             // position of the panel on the page
@@ -82,6 +82,11 @@ Optional settings for each panel::
     // options are omero.model.LengthI.SYMBOLS.keys()
     "pixel_size_x_unit": 'MICROMETER',
 
+    // pixel size z to show z position in labels
+    "pixel_size_z": 0.32,
+    "pixel_size_z_symbol": 'µm',    // µm by default
+    "pixel_size_z_unit": 'MICROMETER',
+
     // show a scalebar
     "scalebar": {
         "show": true,
@@ -108,12 +113,22 @@ Optional settings for each panel::
             "color": "00FF00"
         },
         {
-            // 'live' timestamps, 'time' one of: index (show 1-based T index), milliseconds,
+            // Dynamic properties: text in labels in the form '[property.format]'
+            // are dynamically replaced by the specified values
+
+            // for 'time' property, 'format' one of: index (show 1-based T index), milliseconds,
             // secs, mins:secs, mins, hrs:mins, hrs:mins:secs,
-            "time": "milliseconds",
+            "text": "[time.milliseconds]",
             "size": "12",
             "position": "topleft",
             "color": "FFFFFF"
+        },
+        {
+            // for 'x' and 'y' property, 'format' one of: pixel, unit
+            "text": "X: [x.pixel] - Y: [y.pixel]",
+            "size": "12",
+            "position": "topright",
+            "color": "FFFFFF"
         }
     ],
 
@@ -137,6 +152,8 @@ Optional settings for each panel::
 
     // panel rotation in degrees clockwise
     rotation: 0,
+    // rotation symbol to display in label
+    rotation_symbol:'°',
 
 
 Optional settings for the top-level figure object. If not specified,
@@ -208,6 +225,11 @@ that lines will not appear thicker on a panel when it is zoomed in. Supported Sh
 Version history
 ----------------
 
+New in version 6:
+
+- 'label': 'time':'seconds' changed to 'text':'[time.seconds]' (for all timestamp formats)
+- 'panel': z pixel properties added ('pixel_size_z', 'pixel_size_z_symbol', 'pixel_size_z_unit')
+
 New in version 5:
 
 - `scalebar`: added 'pixel_size_x_unit': "MICROMETER". 

omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

@@ -28,6 +28,7 @@
 import zipfile
 from math import atan2, atan, sin, cos, sqrt, radians, floor, ceil
 from copy import deepcopy
+import re
 
 from omero.model import ImageAnnotationLinkI, ImageI, LengthI
 import omero.scripts as scripts
@@ -1092,23 +1093,27 @@ def get_time_label_text(self, delta_t, format):
         is_negative = delta_t < 0
         delta_t = abs(delta_t)
         text = "%d s" % int(round(delta_t))
-        if format == "milliseconds":
+        if format in ["milliseconds", "ms"]:
             text = "%s ms" % int(round(delta_t * 1000))
-        elif format == "mins":
+        elif format in ["secs", "seconds", "s"]:
+            text = "%d s" % int(round(delta_t))
+        elif format in ["mins", "minutes", "m"]:
             text = "%s mins" % int(round(delta_t / 60))
-        elif format == "mins:secs":
+        elif format in ["mins:secs", "m:s"]:
             m = int(delta_t // 60)
             s = round(delta_t % 60)
             text = "%s:%02d" % (m, s)
-        elif format == "hrs:mins":
+        elif format in ["hrs:mins", "h:m"]:
             h = int(delta_t // 3600)
             m = int(round((delta_t % 3600) / 60))
             text = "%s:%02d" % (h, m)
-        elif format == "hrs:mins:secs":
+        elif format in ["hrs:mins:secs", "h:m:s"]:
             h = int(delta_t // 3600)
             m = (delta_t % 3600) // 60
             s = round(delta_t % 60)
             text = "%s:%02d:%02d" % (h, m, s)
+        else:  # Format unknown
+            return ""
         if text in ["0 s", "0:00", "0 mins", "0:00:00"]:
             is_negative = False
         return ('-' if is_negative else '') + text
@@ -1136,6 +1141,8 @@ def draw_labels(self, panel, page):
         width = panel['width']
         height = panel['height']
 
+        viewport_region = self.get_crop_region(panel)
+
         # Handle page offsets
         x = x - page['x']
         y = y - page['y']
@@ -1148,18 +1155,122 @@ def draw_labels(self, panel, page):
                      'topleft': [], 'topright': [],
                      'bottomleft': [], 'bottomright': []}
 
+        parse_re = re.compile(r"\[.+?\]")
         for l in labels:
-            if 'text' not in l:
-                the_t = panel['theT']
-                timestamps = panel.get('deltaT')
-                if l.get('time') == "index":
-                    l['text'] = str(the_t + 1)
-                elif timestamps and panel['theT'] < len(timestamps):
-                    d_t = panel['deltaT'][the_t]
-                    l['text'] = self.get_time_label_text(d_t, l['time'])
-                else:
-                    continue
-
+            # Substitution of special label by their values
+            new_text = []
+            last_idx = 0
+            for item in parse_re.finditer(l['text']):
+                new_text.append(l['text'][last_idx:item.start()])
+                expr = item.group()[1:-1].split(".")
+                label_value = ""
+
+                if expr[0] in ["time", "t"]:
+                    the_t = panel['theT']
+                    timestamps = panel.get('deltaT')
+                    # default to index
+                    if len(expr) == 1 or expr[1] == "index":
+                        label_value = str(the_t + 1)
+                    else:
+                        if timestamps and the_t < len(timestamps):
+                            d_t = timestamps[the_t]
+                        else:
+                            d_t = 0
+                        label_value = self.get_time_label_text(d_t, expr[1])
+
+                elif expr[0] == "image":
+                    format = expr[1] if len(expr) > 1 else "name"
+                    if format == "name":
+                        label_value = panel['name'].split('/')[-1]
+                    elif format == "id":
+                        label_value = str(panel['imageId'])
+                    # Escaping "_" for markdown
+                    label_value = label_value.replace("_", "\\_")
+
+                elif expr[0] == "dataset":
+                    format = expr[1] if len(expr) > 1 else "name"
+                    if format == "name":
+                        if panel['datasetName']:
+                            label_value = panel['datasetName']
+                        else:
+                            label_value = "No/Many Datasets"
+                    elif format == "id":
+                        if panel['datasetId']:
+                            label_value = panel['datasetName']
+                        else:
+                            label_value = "null"
+                    # Escaping "_" for markdown
+                    label_value = label_value.replace("_", "\\_")
+
+                elif expr[0] in ['x', 'y', 'z', 'width', 'height',
+                                 'w', 'h', 'rotation', 'rot']:
+                    format = expr[1] if len(expr) > 1 else "pixel"
+                    if format == "px":
+                        format = "pixel"
+                    prop = expr[0]
+                    if prop == "w":
+                        prop = "width"
+                    elif prop == "h":
+                        prop = "height"
+                    elif prop == "rot":
+                        prop = "rotation"
+
+                    if prop == "z":
+                        size_z = panel.get('sizeZ')
+                        pixel_size_z = panel.get('pixel_size_z')
+                        z_symbol = panel.get('pixel_size_z_symbol')
+                        if pixel_size_z is None:
+                            pixel_size_z = 0
+
+                        if ("z_projection" in panel.keys()
+                           and panel["z_projection"]):
+                            z_start, z_end = panel["z_start"], panel["z_end"]
+                            if format == "pixel":
+                                label_value = (str(z_start + 1) + "-"
+                                               + str(z_end + 1))
+                            elif format == "unit" and size_z:
+                                z_start = f"{(z_start * pixel_size_z):.2f}"
+                                z_end = f"{(z_end * pixel_size_z):.2f}"
+                                label_value = (z_start + " " + z_symbol + " - "
+                                               + z_end + " " + z_symbol)
+                        else:
+                            the_z = panel['theZ'] if panel['theZ'] else 0
+                            if format == "pixel":
+                                label_value = str(the_z + 1)
+                            elif (format == "unit" and size_z
+                                  and the_z < size_z):
+                                z_pos = f"{(the_z * pixel_size_z):.2f}"
+                                label_value = (z_pos + " " + z_symbol)
+
+                    elif prop == "rotation":
+                        label_value = (str(int(panel["rotation"]))
+                                       + panel['rotation_symbol'])
+
+                    else:
+                        value = viewport_region[prop]
+                        if format == "pixel":
+                            label_value = str(int(value))
+                        elif format == "unit":
+                            if prop in ['x', 'width']:
+                                scale = panel['pixel_size_x']
+                            elif prop in ['y', 'height']:
+                                scale = panel['pixel_size_y']
+                            rounded = f"{(value * scale):.2f}"
+                            label_value = ("" + rounded +
+                                           " " + panel['pixel_size_x_symbol'])
+
+                elif expr[0] in ["channels", "c"]:
+                    label_value = []
+                    for channel in panel["channels"]:
+                        if channel["active"]:
+                            label_value.append(channel["label"])
+                    label_value = " ".join(label_value)
+
+                new_text.append(label_value if label_value else item.group())
+                last_idx += item.end()
+
+            new_text.append(l['text'][last_idx:])
+            l['text'] = "".join(new_text)
             pos = l['position']
             l['size'] = int(l['size'])   # make sure 'size' is number
             # If page is black and label is black, make label white

omero_figure/static/figure/css/figure.css

@@ -167,29 +167,13 @@
         padding: 3px 15px;
     }
 
-    .markdown-info {
-        padding: 3px 12px;
-        color: #aaa;
-        text-align: right;
-        padding-left: 40px;
-        background: url(../images/markdown_light32x20.png) 0% center no-repeat;
-    }
-    .markdown-info:hover {
-        background: url(../images/markdown_dark32x20.png) 0% center no-repeat;
-    }
     .legend-container .markdown-info {
         display: none;
     }
     .legend-container .editing .markdown-info {
         display: block;
     }
 
-    #labelsTab .markdown-info {
-        height: 18px;
-        margin: 9px 9px 0;
-        float: left"
-    }
-
     /* hide appropriate collapse/hide button */
     .legend-collapsed .collapse-legend{
         display: none;

omero_figure/templates/figure/index.html

@@ -514,9 +514,10 @@ <h4 class="modal-title" id="addImagesLabel">Import from JSON</h4>
             <div class="modal-content">
                 <div class="modal-header">
                     <button type="button" class="close" data-dismiss="modal" aria-hidden="true">&times;</button>
-                    <h4 class="modal-title">Markdown Formatting</h4>
+                    <h4 class="modal-title">Label Formatting</h4>
                 </div>
-                <div class="modal-body">
+                <div class="modal-body" style="max-height:518px">
+                    <h4>Markdown formatting</h4>
                     <p>
                         You can use "Markdown" syntax to add formatting to plain text. For example,
                         **this text will be bold** and this *word* will be italic. NB: Links are not
@@ -545,6 +546,52 @@ <h4 class="modal-title">Markdown Formatting</h4>
                         </tr>
                        <!--  <tr><td>You need to use 2 line breaks between paragraphs</td><td></td></tr> -->
                     </table>
+                    <h4>Dynamic properties</h4>
+                    <p>
+                        The drop-down menu in the 'Add Labels' form allows you to create labels based on Image metadata. 
+                        Labels created with square brackets indicate dynamic properties. The properties within the square 
+                        brackets will be dynamically updated upon changes. Additional text can be added outside the square 
+                        brackets and will not be affected when the labels are displayed.<br>
+                        The following table shows some examples, including the use of dynamic properties and markdown together.
+                    </p>
+                    <table class="table">
+                        <tr>
+                            <td></td>
+                            <th>This text will be formatted to...</th>
+                            <th>...this text</th></tr>
+                        <tr>
+                        <tr>
+                            <th>X and Y in pixels</th>
+                            <td>X:[x.pixel] - Y:[y.pixel]</td>
+                            <td>X:52 - Y:89</td>
+                        </tr>
+                        <tr>
+                            <th>X and Y in units</th>
+                            <td>X:[x.unit] - Y:[y.unit]</td>
+                            <td>X:0.43 &#181;m - Y:0.23 &#181;m</td>
+                        </tr>
+                        <tr>
+                            <th>Width</th>
+                            <td>Width: [width.pixel]</td>
+                            <td>Width: 400</td>
+                        </tr>
+                        <tr>
+                            <th>Height (with markdown formatting)</th>
+                            <td>*Height*: **[height.pixel]**</td>
+                            <td><i>Height</i>: <strong>300</strong></td>
+                        </tr>
+                        <tr>
+                            <th>Image ID</th>
+                            <td>Image ID: [image.id]</td>
+                            <td>Image ID: 23556</td>
+                        </tr>
+                        <tr>
+                            <th>Dataset ID</th>
+                            <td>Dataset ID: [dataset.id]</td>
+                            <td>Dataset ID: 1654</td>
+                        </tr>
+                    </table>
+                    <h4>Legend</h4>
                     <p>The figure legend will be included in the PDF info page when the figure is
                         exported.</p>
                 </div>
@@ -1020,7 +1067,9 @@ <h5>Scalebar</h5>
                     <h5 style="float: left">Add Labels</h5>
 
                     <button type="button" class="btn btn-link markdown-info"
-                        title="Use Markdown formatting. Click for more info..."></button>
+                        title="Show label formatting options...">
+                        Tips
+                    </button>
                     <div class="clearfix"></div>
                     <form class="new-label-form form-inline" role="form">
                     </form>

omero_figure/urls.py

@@ -73,6 +73,10 @@
     # Use query ?image=1&image=2
     url(r'^timestamps/$', views.timestamps, name='figure_timestamps'),
 
+    # Get Z scale for images
+    # Use query ?image=1&image=2
+    url(r'^z_scale/$', views.z_scale, name='figure_z_scale'),
+
     url(r'^roiCount/(?P<image_id>[0-9]+)/$', views.roi_count,
         name='figure_roiCount'),