Merge pull request #210 from will-moore/export_to_omero

Export to omero

omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

@@ -19,6 +19,7 @@
 import logging
 import json
 import unicodedata
+import numpy
 
 from datetime import datetime
 import os
@@ -58,8 +59,7 @@
     reportlab_installed = True
 except ImportError:
     reportlab_installed = False
-    logger.error("Reportlab not installed. See"
-                 " https://pypi.python.org/pypi/reportlab/")
+    logger.error("Reportlab not installed.")
 
 
 ORIGINAL_DIR = "1_originals"
@@ -214,7 +214,8 @@ def draw_rectangle(self, shape):
         g = float(rgb[1])/255
         b = float(rgb[2])/255
         self.canvas.setStrokeColorRGB(r, g, b)
-        stroke_width = shape['strokeWidth'] * self.scale
+        stroke_width = shape['strokeWidth'] if 'strokeWidth' in shape else 2
+        stroke_width = stroke_width * self.scale
         self.canvas.setLineWidth(stroke_width)
 
         rotation = self.panel['rotation'] * -1
@@ -482,7 +483,7 @@ def draw_line(self, shape):
 
     def draw_rectangle(self, shape):
         # clockwise list of corner points on the OUTSIDE of thick line
-        w = shape['strokeWidth']
+        w = shape['strokeWidth'] if 'strokeWidth' in shape else 2
         cx = shape['x'] + (shape['width']/2)
         cy = shape['y'] + (shape['height']/2)
         rotation = self.panel['rotation'] * -1
@@ -583,13 +584,15 @@ def get_zip_name(self):
         name = name.replace(",", ".")
         return "%s.zip" % name
 
-    def get_figure_file_name(self):
+    def get_figure_file_name(self, page=None):
         """
         For PDF export we will only create a single figure file, but
         for TIFF export we may have several pages, so we need unique names
         for each to avoid overwriting.
         This method supports both, simply using different extension
         (pdf/tiff) for each.
+
+        @param page:        If we know a page number we want to use.
         """
 
         # Extension is pdf or tiff
@@ -610,7 +613,7 @@ def get_figure_file_name(self):
         # Remove commas: causes problems 'duplicate headers' in file download
         full_name = full_name.replace(",", ".")
 
-        index = 1
+        index = page if page is not None else 1
         if fext == "tiff" and self.page_count > 1:
             full_name = "%s_page_%02d.%s" % (name, index, fext)
         if self.zip_folder_name is not None:
@@ -691,7 +694,7 @@ def build_figure(self):
             self.add_panels_to_page(panels_json, image_ids, page)
 
             # complete page and save
-            self.save_page()
+            self.save_page(p)
 
             col = col + 1
             if col >= page_col_count:
@@ -701,14 +704,17 @@ def build_figure(self):
         # Add thumbnails and links page
         self.add_info_page(panels_json)
 
-        # Saves the completed  figure file
+        # Saves the completed figure file
         self.save_figure()
 
         # PDF will get created in this group
         if group_id is None:
             group_id = self.conn.getEventContext().groupId
         self.conn.SERVICE_OPTS.setOmeroGroup(group_id)
 
+        return self.create_file_annotation(image_ids)
+
+    def create_file_annotation(self, image_ids):
         output_file = self.figure_file_name
         ns = self.ns
         mimetype = self.mimetype
@@ -1120,6 +1126,8 @@ def draw_panel(self, panel, page, idx):
         y = y - page['y']
 
         image = self.conn.getObject("Image", image_id)
+        if image is None:
+            return None, None
         self.apply_rdefs(image, channels)
 
         # create name to save image
@@ -1147,6 +1155,8 @@ def get_thumbnail(self, image_id):
 
         conn = self.conn
         image = conn.getObject("Image", image_id)
+        if image is None:
+            return
         thumb_data = image.getThumbnail(size=(96, 96))
         i = StringIO(thumb_data)
         pil_img = Image.open(i)
@@ -1306,6 +1316,8 @@ def add_panels_to_page(self, panels_json, image_ids, page):
             # For TIFF export, draw_panel() also adds shapes to the
             # PIL image before pasting onto the page...
             image, pil_img = self.draw_panel(panel, page, i)
+            if image is None:
+                continue
             if image.canAnnotate():
                 image_ids.add(image_id)
             # ... but for PDF we have to add shapes to the whole PDF page
@@ -1329,7 +1341,7 @@ def create_figure(self):
         self.figure_canvas = canvas.Canvas(
             name, pagesize=(self.page_width, self.page_height))
 
-    def save_page(self):
+    def save_page(self, page=None):
         """ Called on completion of each page. Saves page of PDF """
         self.figure_canvas.showPage()
 
@@ -1656,7 +1668,7 @@ def draw_text(self, text, x, y, fontsize, rgb, align="center"):
         # Use label as mask, so transparent part is not pasted
         self.tiff_figure.paste(temp_label, (x, y), mask=temp_label)
 
-    def save_page(self):
+    def save_page(self, page=None):
         """
         Save the current PIL image page as a TIFF and start a new
         PIL image for the next page
@@ -1695,6 +1707,68 @@ def save_figure(self):
         self.figure_canvas.save()
 
 
+class OmeroExport(TiffExport):
+
+    def __init__(self, conn, script_params):
+
+        super(OmeroExport, self).__init__(conn, script_params)
+
+        self.new_image = None
+
+    def save_page(self, page=None):
+        """
+        Save the current PIL image page as a new OMERO image and start a new
+        PIL image for the next page
+        """
+        self.figure_file_name = self.get_figure_file_name(page + 1)
+
+        # Try to get a Dataset
+        dataset = None
+        for panel in self.figure_json['panels']:
+            parent = self.conn.getObject('Image', panel['imageId']).getParent()
+            if parent is not None and parent.OMERO_CLASS == 'Dataset':
+                if parent.canLink():
+                    dataset = parent
+                    break
+
+        # Need to specify group for new image
+        group_id = self.conn.getEventContext().groupId
+        if dataset is not None:
+            group_id = dataset.getDetails().group.id.val
+            dataset = dataset._obj      # get the omero.model.DatasetI
+        self.conn.SERVICE_OPTS.setOmeroGroup(group_id)
+
+        description = "Created from OMERO.figure: "
+        url = self.script_params.get("Figure_URI")
+        legend = self.figure_json.get('legend')
+        if url is not None:
+            description += url
+        if legend is not None:
+            description = "%s\n\n%s" % (description, legend)
+
+        np_array = numpy.asarray(self.tiff_figure)
+        red = np_array[::, ::, 0]
+        green = np_array[::, ::, 1]
+        blue = np_array[::, ::, 2]
+        plane_gen = iter([red, green, blue])
+        self.new_image = self.conn.createImageFromNumpySeq(
+            plane_gen,
+            self.figure_file_name,
+            sizeC=3,
+            description=description, dataset=dataset)
+        # Reset group context
+        self.conn.SERVICE_OPTS.setOmeroGroup(-1)
+        # Create a new blank tiffFigure for subsequent pages
+        self.create_figure()
+
+    def create_file_annotation(self, image_ids):
+        """Return result of script."""
+
+        # We don't need to create file annotation, but we can return
+        # the new image, which will be returned from the script
+        return self.new_image
+
+
 def export_figure(conn, script_params):
 
     # make sure we can find all images
@@ -1710,7 +1784,8 @@ def export_figure(conn, script_params):
         fig_export = TiffExport(conn, script_params)
     elif export_option == 'TIFF_IMAGES':
         fig_export = TiffExport(conn, script_params, export_images=True)
-
+    elif export_option == 'OMERO':
+        fig_export = OmeroExport(conn, script_params)
     return fig_export.build_figure()
 
 
@@ -1721,7 +1796,8 @@ def run_script():
     """
 
     export_options = [rstring('PDF'), rstring('PDF_IMAGES'),
-                      rstring('TIFF'), rstring('TIFF_IMAGES')]
+                      rstring('TIFF'), rstring('TIFF_IMAGES'),
+                      rstring('OMERO')]
 
     client = scripts.client(
         'Figure_To_Pdf.py',
@@ -1756,10 +1832,10 @@ def run_script():
         file_annotation = export_figure(conn, script_params)
 
         # return this file_annotation to the client.
-        client.setOutput("Message", rstring("Pdf Figure created"))
+        client.setOutput("Message", rstring("Figure created"))
         if file_annotation is not None:
             client.setOutput(
-                "File_Annotation",
+                "New_Figure",
                 robject(file_annotation._obj))
 
     finally:

omero_figure/static/figure/css/figure.css

@@ -718,6 +718,14 @@
         transform: rotate(90deg);
     }
 
+    @keyframes spin {
+        100% { -webkit-transform: rotate(360deg); transform:rotate(360deg); }
+    }
+
+    .navbar-right .glyphicon-refresh {
+        animation: spin 2s linear infinite;
+        padding: 2px 2px 5px 2px;
+    }
 
     .colorpicker span,
     .label-color span:first-child,

omero_figure/templates/figure/index.html

@@ -711,12 +711,14 @@ <h4 class="modal-title">Open</h4>
 
                     <button id="pdf_inprogress" style="display:none" class="btn btn-primary btn-sm"
                             title="Figure generation in progress..." onClick="return false;">
-                        Exporting Figure...
+                        Exporting Figure
+                        <span class="glyphicon glyphicon-refresh"></span>
                     </button>
 
-                    <a id="pdf_download" href="#" target="download_pdf"
+                    <a id="pdf_download" href="#" target="_blank"
                             style="padding: 4px 10px; display: none;"
                             class="btn btn-primary btn-sm script-result" title="Download Figure">
+                        <!-- Tooltip and glyphicon also set on script completion in figure_view.js -->
                         <span class="glyphicon glyphicon-download-alt" style="font-size: 14px"></span>
                     </a>
 
@@ -759,6 +761,11 @@ <h4 class="modal-title">Open</h4>
                                 <span class="glyphicon glyphicon-ok" style="color:#333; visibility:hidden"></span>
                                 TIFF with images</a>
                             </li>
+                            <li><a href="#" data-export-option="to OMERO"
+                                    title="Export each page as an Image in OMERO">
+                                <span class="glyphicon glyphicon-ok" style="color:#333; visibility:hidden"></span>
+                                New OMERO Image</a>
+                            </li>
                         </ul>
                     </div>
                 </form>

src/js/views/figure_view.js

@@ -168,7 +168,8 @@
             opts = {"PDF": "PDF",
                 "PDF & images": "PDF_IMAGES",
                 "TIFF": "TIFF",
-                "TIFF & images": "TIFF_IMAGES"};
+                "TIFF & images": "TIFF_IMAGES",
+                "to OMERO": "OMERO"};
             exportOption = opts[export_opt];
 
             // Get figure as json
@@ -214,10 +215,22 @@
                                 $pdf_inprogress.hide();
 
                                 // Show result
-                                if (pdf_job.results.File_Annotation) {
-                                    var fa_id = pdf_job.results.File_Annotation.id,
-                                        fa_download = WEBINDEX_URL + "annotation/" + fa_id + "/";
-                                    $pdf_download.attr('href', fa_download).show();
+                                if (pdf_job.results.New_Figure) {
+                                    var fa_id = pdf_job.results.New_Figure.id;
+                                    if (pdf_job.results.New_Figure.type === "FileAnnotation") {
+                                        var fa_download = WEBINDEX_URL + "annotation/" + fa_id + "/";
+                                        $pdf_download
+                                            .attr({'href': fa_download, 'data-original-title': 'Download Figure'})
+                                            .show()
+                                            .children('span').prop('class', 'glyphicon glyphicon-download-alt');
+                                    } else if (pdf_job.results.New_Figure.type === "Image") {
+                                        var fa_download = pdf_job.results.New_Figure.browse_url;
+                                        $pdf_download
+                                            .attr({'href': fa_download, 'data-original-title': 'Go to Figure Image'})
+                                            .show()
+                                            .tooltip()
+                                            .children('span').prop('class', 'glyphicon glyphicon-share');
+                                    }
                                 } else if (pdf_job.stderr) {
                                     // Only show any errors if NO result
                                     var stderr_url = WEBINDEX_URL + "get_original_file/" + pdf_job.stderr + "/";