Merge branch 'master' into update_readme

.github/workflows/publish_pypi.yml

@@ -9,6 +9,8 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
       - name: Build a binary wheel and a source tarball
         run: |
           python -mpip install wheel

Dockerfile

@@ -10,7 +10,6 @@ RUN npm install -g grunt-cli && npm install grunt --save-dev
 RUN $(npm bin)/grunt build
 RUN /opt/omero/web/venv3/bin/pip install -e .
 
-
 RUN echo "config set omero.web.application_server development" >> /opt/omero/web/config/01-default-webapps.omero
 RUN echo "config set omero.web.debug true" >> /opt/omero/web/config/01-default-webapps.omero
 USER omero-web

docs/figure_file_format.rst

@@ -105,7 +105,7 @@ Optional settings for each panel::
     ],
 
     // labels on the panel
-    // positions are: top, left, right, leftvert, bottom, topleft, topright, bottomleft, bottomright
+    // positions are: top, left, right, leftvert, rightvert, bottom, topleft, topright, bottomleft, bottomright
     "labels": [
         {
             "text": "GFP-INCENP",

omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

@@ -573,7 +573,7 @@ def draw_shape_label(self, shape, bounds):
         except Exception:
             font = ImageFont.load(
                 '%s/pilfonts/B%0.2d.pil' % (self.GATEWAYPATH, size))
-        textsize = font.getsize(text)
+        textsize = font.getbbox(text)[2:]
         xy = (center[0] - textsize[0] / 2.0, center[1] - textsize[1] / 2.0)
         self.draw.text(xy, text, fill=rgba, font=font)
 
@@ -1153,7 +1153,7 @@ def draw_labels(self, panel, page):
 
         # group by 'position':
         positions = {'top': [], 'bottom': [], 'left': [],
-                     'leftvert': [], 'right': [],
+                     'leftvert': [], 'right': [], 'rightvert': [],
                      'topleft': [], 'topright': [],
                      'bottomleft': [], 'bottomright': []}
 
@@ -1247,6 +1247,7 @@ def draw_labels(self, panel, page):
                         z_symbol = panel.get('pixel_size_z_symbol')
                         if pixel_size_z is None:
                             pixel_size_z = 0
+                        if z_symbol is None:
                             z_symbol = "\xB5m"
 
                         if ("z_projection" in panel.keys()
@@ -1265,9 +1266,13 @@ def draw_labels(self, panel, page):
                         else:
                             the_z = panel['theZ'] if panel['theZ'] else 0
                             if format == "pixel":
+                                if offset is not None and 1 <= offset:
+                                    the_z -= offset
                                 label_value = str(the_z + 1)
                             elif (format == "unit" and size_z
                                   and the_z < size_z):
+                                if offset is not None and 1 <= offset:
+                                    the_z -= offset
                                 z_pos = "%.*f" % (precision,
                                                   (the_z * pixel_size_z))
                                 label_value = (z_pos + " " + z_symbol)
@@ -1299,6 +1304,8 @@ def draw_labels(self, panel, page):
                             label_value.append(channel["label"])
                     label_value = " ".join(label_value)
 
+                elif prop_nf[0] in ["zoom"]:
+                    label_value = str(panel["zoom"]) + " %"
                 new_text.append(label_value if label_value else item.group())
                 last_idx = item.end()
 
@@ -1310,7 +1317,7 @@ def draw_labels(self, panel, page):
             page_color = self.figure_json.get('page_color', 'ffffff').lower()
             label_color = label['color'].lower()
             label_on_page = pos in ('left', 'right', 'top',
-                                    'bottom', 'leftvert')
+                                    'bottom', 'leftvert', 'rightvert')
             if label_on_page:
                 if label_color == '000000' and page_color == '000000':
                     label['color'] = 'ffffff'
@@ -1396,6 +1403,13 @@ def draw_lab(label, lx, ly, align='left'):
                 for label in labels:
                     lx = lx - label['size'] - spacer
                     draw_lab(label, lx, ly, align='vertical')
+            elif key == 'rightvert':
+                lx = x + width + spacer
+                ly = y + (height/2)
+                labels.reverse()
+                for label in labels:
+                    lx = lx + label['size'] + spacer
+                    draw_lab(label, lx, ly, align='right-vertical')
 
     def draw_scalebar(self, panel, region_width, page):
         """
@@ -2024,7 +2038,7 @@ def draw_text(self, text, x, y, fontsize, rgb, align="center"):
             x = x - para_width
         elif (align == "left"):
             pass
-        elif align == 'vertical':
+        elif align == 'left-vertical':
             # Switch axes
             c.rotate(90)
             px = x
@@ -2033,6 +2047,15 @@ def draw_text(self, text, x, y, fontsize, rgb, align="center"):
             # Align center
             alignment = TA_CENTER
             x = x - (para_width/2)
+        elif align == 'right-vertical':
+            # Switch axes
+            c.rotate(-90)
+            px = x
+            x = -y
+            y = px
+            # Align center
+            alignment = TA_CENTER
+            x = x - (para_width/2)
 
         # set fully opaque background color to avoid transparent text
         c.setFillColorRGB(0, 0, 0, 1)
@@ -2050,8 +2073,10 @@ def draw_text(self, text, x, y, fontsize, rgb, align="center"):
         para.drawOn(c, x, y - h + int(fontsize * 0.25))
 
         # Rotate back again
-        if align == 'vertical':
+        if align == 'left-vertical':
             c.rotate(-90)
+        elif align == 'right-vertical':
+            c.rotate(90)
 
     def draw_scalebar_line(self, x, y, x2, y2, width, rgb):
         """ Adds line to PDF. Overwritten for TIFF below """
@@ -2230,7 +2255,7 @@ def draw_temp_label(self, text, fontsize, rgb):
         heights = []
         for t in tokens:
             font = self.get_font(fontsize, t['bold'], t['italics'])
-            txt_w, txt_h = font.getsize(t['text'])
+            txt_w, txt_h = font.getbbox(t['text'])[2:]
             widths.append(txt_w)
             heights.append(txt_h)
 
@@ -2243,7 +2268,7 @@ def draw_temp_label(self, text, fontsize, rgb):
         w = 0
         for t in tokens:
             font = self.get_font(fontsize, t['bold'], t['italics'])
-            txt_w, txt_h = font.getsize(t['text'])
+            txt_w, txt_h = font.getbbox(t['text'])[2:]
             textdraw.text((w, 0), t['text'], font=font, fill=rgb)
             w += txt_w
         return temp_label
@@ -2308,9 +2333,13 @@ def draw_text(self, text, x, y, fontsize, rgb, align="center"):
 
         temp_label = self.draw_temp_label(text, fontsize, rgb)
 
-        if align == "vertical":
+        if align == "left-vertical":
             temp_label = temp_label.rotate(90, expand=True)
             y = y - (temp_label.size[1]/2)
+        elif align == "right-vertical":
+            temp_label = temp_label.rotate(-90, expand=True)
+            y = y - (temp_label.size[1]/2)
+            x = x - temp_label.size[0]
         elif align == "center":
             x = x - (temp_label.size[0] / 2)
         elif align == "right":

omero_figure/static/figure/css/figure.css

@@ -123,7 +123,7 @@
         line-height: 20px;
         padding: 12px;
         position: absolute;
-        right: 450px;
+        right: 520px;
         text-align: center;
         height: 100%;
     }
@@ -233,6 +233,11 @@
         height: 14px;
         border-radius: 5px;
     }
+    #vp_zoom_value {
+        float: right;
+        width: 50px;
+        margin-top: 5px;
+    }
     .toggle_channel {
         border-radius: 6px 6px 6px 6px;
         margin: 2px;
@@ -344,6 +349,9 @@
     .left_vlabels>div {
         margin-bottom: 5px;
     }
+    .right_vlabels>div {
+        margin-bottom: 5px;
+    }
     .label_middle, .label_middle table, .label_middle td {
         height:100%;
         width:10000px;
@@ -362,11 +370,26 @@
         -webkit-transform: rotate(-90deg);
         transform: rotate(-90deg);
     }
+    .right_vlabels{
+        position: absolute;
+        left: 100%;
+        height: 300%;
+        top: -100%;
+        width: 300%;
+        text-align: center;
+        -webkit-transform: rotate(90deg);
+        transform: rotate(90deg);
+    }
     .left_vlabels>div {
         position: absolute;
         bottom:0;
         width:100%;
     }
+    .right_vlabels>div {
+        position: absolute;
+        bottom:0;
+        width:100%;
+    }
 
     .previewIdChange .glyphicon-ok {
         color: #0f0;
@@ -705,6 +728,10 @@
     .navbar>div.container {
         max-width: 100%;
     }
+    #alignment-toolbars {
+        padding-right: 0;
+        margin-right: -20px;
+    }
     /** Add my class to boost size of font icons **/
     .icon-buttons {
         margin-right: 20px;

omero_figure/templates/figure/index.html

@@ -520,8 +520,14 @@ <h4 class="modal-title">Label Formatting</h4>
                     <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
-                        supported for panel labels.
+                        **this text will be bold** and this *word* will be italic. 
+                    </p>
+                    <p>
+                        NB: Links are not supported for panel labels.
+                    </p>
+                    <p>
+                        NB: You can escape a certain character to not be interpreted as Markdown by adding \ in front of the 
+                        character. Ex: "my_string_" is interpreted as "my<i>string</i>" but "my\_string\_" is now interpreted as "my_string_"
                     </p>
 
                     <table class="table">
@@ -531,21 +537,21 @@ <h4>Markdown formatting</h4>
                             <th>...this text</th></tr>
                         <tr>
                             <th>BOLD</th>
-                            <td>Use 2 stars for **bold**.</td>
-                            <td>Use 2 stars for <strong>bold</strong>.</td>
+                            <td>**bold** or __bold__</td>
+                            <td><strong>bold</strong> or <strong>bold</strong></td>
                         </tr>
                         <tr>
                             <th>ITALIC</th>
-                            <td>Use 1 star for *italic*.</td>
-                            <td>Use 1 star for <i>italic</i>.</td>
+                            <td>*italic* or _italic_</td>
+                            <td><i>italic</i> or <i>italic</i></td>
                         </tr>
                         <tr>
                             <th>LINKS</th>
-                            <td>Add links with [Link text](http://link_url.com)</td>
-                            <td>Add links with <a href="#">Link text</a></td>
+                            <td>[Link text](http://link_url.com)</td>
+                            <td><a href="#">Link text</a></td>
                         </tr>
                        <!--  <tr><td>You need to use 2 line breaks between paragraphs</td><td></td></tr> -->
-                    </table>
+                    </table>                    
                     <h4>Dynamic properties</h4>
                     <p>
                         The drop-down menu in the 'Add Labels' form allows you to create labels based on Image metadata. 
@@ -595,6 +601,16 @@ <h4>Dynamic properties</h4>
                             <td>Time: [time.seconds; precision=2; offset=3]</td>
                             <td>Time: -0.06 s</td>
                         </tr>
+                        <tr>
+                            <th>Z index with units <br/> (first plane is Z: 0.00 &#181;m), <br/>offset by 3 times the Z pixel size</th>
+                            <td>Z: [z.unit; offset=3]</td>
+                            <td>Z: -3.00 &#181;m </td>
+                        </tr>
+                        <tr>
+                            <th>Z index (first plane is Z: 1) <br/>offset by 3</th>
+                            <td>Z: [z.pixel; offset=3]</td>
+                            <td>Z: -2 </td>
+                        </tr>
                         <tr>
                             <th>Image ID</th>
                             <td>Image ID: [image.id]</td>
@@ -605,6 +621,11 @@ <h4>Dynamic properties</h4>
                             <td>Dataset ID: [dataset.id]</td>
                             <td>Dataset ID: 1654</td>
                         </tr>
+                        <tr>
+                            <th>Zoom</th>
+                            <td>[zoom]</td>
+                            <td>100 %</td>
+                        </tr>
                     </table>
                     <h4>Legend</h4>
                     <p>The figure legend will be included in the PDF info page when the figure is
@@ -698,8 +719,14 @@ <h4 class="modal-title" id="addImagesLabel">Labels from Key-Value Pairs</h4>
                 </div>
                 <form class="labelsFromMapAnnsForm" role="form">
                     <div class="modal-body">
-                        <p>Choose Key
-                            <small class="text-muted">(shows numbers of images)</small>:</p>
+                        <div>                                                    
+                            <input type="radio" id="all-keys" name="kvpChoice" value="all-keys" />
+                            <label for="all-keys">All Keys </label>
+
+                            <input type="radio" id="single-key" name="kvpChoice" value="single-key" checked />
+                            <label for="single-key">Choose Key <small class="text-muted">(shows numbers of images)</small>:</label>
+                        </div>
+
                         <select>
                         </select>
                         <div class="checkbox">
@@ -865,6 +892,9 @@ <h5>Example Label</h5>
                         <button type="button" class="aleft btn btn-default btn-sm" title="Align Left" disabled="disabled">
                             <span class="glyphicon glyphicon-align-left"></span>
                         </button>
+                        <button type="button" class="aright btn btn-default btn-sm" title="Align Right" disabled="disabled">
+                            <span class="glyphicon glyphicon-align-right"></span>
+                        </button>
                         <button type="button" class="agrid btn btn-default btn-sm" title="Align To Grid" disabled="disabled">
                             <span class="glyphicon glyphicon-th"></span>
                         </button>
@@ -890,6 +920,9 @@ <h5>Example Label</h5>
                         <button type="button" class="atop btn btn-default btn-sm rotate-font" title="Align Top" disabled="disabled">
                             <span class="glyphicon glyphicon-align-right"></span>
                         </button>
+                        <button type="button" class="abottom btn btn-default btn-sm rotate-font" title="Align Bottom" disabled="disabled">
+                            <span class="glyphicon glyphicon-align-left"></span>
+                        </button>
                         <button type="button" class="btn btn-default btn-sm dropdown-toggle" title="Align Sizes"
                             disabled="disabled" data-toggle="dropdown">
                             <span class="glyphicon glyphicon-fullscreen"></span>
@@ -1070,12 +1103,14 @@ <h5>Example Label</h5>
                     <div class='clearfix'></div>
                     <div class='tab-footer'>
                         <div class="col-sm-2 no-padding">
-                            <h5>Zoom</h5>
+                            <h5>Zoom %</h5>
                         </div>
                         <div class="col-sm-8 no-padding">
                             <div id="vp_zoom_slider"></div>
                         </div>
-                        <div id="vp_zoom_value" class="col-sm-2" style="padding: 8px 0 0; text-align:right"></div>
+
+                        <input id="vp_zoom_value" type="number" size="4"/>
+
                         <div class='clearfix'></div>
                         <div id="reset-zoom-view">
                             <!-- button added by ZoomView render() -->

omero_figure/views.py

@@ -121,15 +121,19 @@ def img_data_json(request, image_id, conn=None, **kwargs):
 
     if units_support:
         # Add extra parameters with units data
+        if 'pixel_size' not in rv:
+            rv['pixel_size'] = {}
         # NB ['pixel_size']['x'] will have size in MICROMETER
         px = image.getPrimaryPixels().getPhysicalSizeX()
-        rv['pixel_size']['valueX'] = px.getValue()
-        rv['pixel_size']['symbolX'] = px.getSymbol()
-        rv['pixel_size']['unitX'] = str(px.getUnit())
+        if px is not None:
+            rv['pixel_size']['valueX'] = px.getValue()
+            rv['pixel_size']['symbolX'] = px.getSymbol()
+            rv['pixel_size']['unitX'] = str(px.getUnit())
         py = image.getPrimaryPixels().getPhysicalSizeY()
-        rv['pixel_size']['valueY'] = py.getValue()
-        rv['pixel_size']['symbolY'] = py.getSymbol()
-        rv['pixel_size']['unitY'] = str(py.getUnit())
+        if py is not None:
+            rv['pixel_size']['valueY'] = py.getValue()
+            rv['pixel_size']['symbolY'] = py.getSymbol()
+            rv['pixel_size']['unitY'] = str(py.getUnit())
         pz = image.getPrimaryPixels().getPhysicalSizeZ()
         if pz is not None:
             rv['pixel_size']['valueZ'] = pz.getValue()