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added _repr_html_ method for _ImageWrapper #394

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merged 6 commits into from
Apr 24, 2024
Merged

added _repr_html_ method for _ImageWrapper #394

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1fec7e2
added `repr_html` method for `_ImageWrapper`
jo-mueller Jan 30, 2024
1e40b2a
limited floating point precision in voxel dimensions
jo-mueller Jan 31, 2024
48d4de4
Show Image, Dataset and Project in a table
will-moore Feb 1, 2024
b945fdb
Merge pull request #1 from will-moore/repr_html
jo-mueller Feb 1, 2024
da9d644
moved `repr_html` code to utils
jo-mueller Apr 12, 2024
b0a7fad
escaped non-existing pixsizes/units
jo-mueller Apr 18, 2024
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101 changes: 101 additions & 0 deletions src/omero/gateway/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10426,6 +10426,107 @@ def getROICount(self, shapeType=None, filterByCurrentUser=False):
return count[0][0].getValue()
return len(self._get_rois(shapeType, filterByCurrentUser))

def _repr_html_(self):
import base64

html_style_header = """
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Image Details</title>
<style>
img {
min-width: 250px; /* Set the minimum width for all images */
min-height: 250px; /* Set the minimum height for all images */
}
.align-top {
vertical-align: top;
}
.text-right {
text-align: right;
}
</style>
</head>
"""

# create a sub-table for image information
table_imageinfo = f"""
<table>\n
<tr>\n
<td><b>Image name: </b></td> <td class=text-right>{self.getName()}</td>\n
</tr>\n
<tr>\n
<td><b>Image ID: </b></td> <td class=text-right>{self.getId()}</td>\n
</tr>\n
<tr>\n
<td><b>Project ID: </b></td> <td class=text-right>{self.getProject().getId()}</td>\n
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</tr>\n
</table>
"""

# get entries for thumbnail and dimensions
encoded_image = base64.b64encode(self.getThumbnail()).decode('utf-8')
dimensions = f"""(
{self.getSizeT()},
{self.getSizeC()},
{self.getSizeZ()},
{self.getSizeY()},
{self.getSizeX()})"""
physical_dims = """({:.3f}, {:.3f}, {:.3f})""".format(
self.getPixelSizeZ(),
self.getPixelSizeY(),
self.getPixelSizeX())
physical_units = f"""(
{self.getPixelSizeZ(units=True).getUnit()},
{self.getPixelSizeY(units=True).getUnit()},
{self.getPixelSizeX(units=True).getUnit()})"""

table_dimensions = f"""
<table>\n
<tr>\n
<td><b>Dimensions (TCZYX): </b></td> <td class=text-right>{dimensions}</td>\n
</tr>\n
<tr>\n
<td><b>Voxel/Pixel dimensions (ZYX): </b></td> <td class=text-right>{physical_dims}</td>\n
</tr>\n
<tr>\n
<td><b>Physical units: </b></td> <td class=text-right>{physical_units}</td>\n
</tr>\n
<tr>\n
<td><b>Channel Names: </b></td> <td class=text-right>{self.getChannelLabels()}</td>\n
</tr>\n
</table>
"""

table_assembly = f"""
<table>
<tr>
<td><div class="thumbnail">
<img src="data:image/jpeg;base64,{encoded_image}" alt="Thumbnail">
</div></td>
<td class="align-top"><h2>Image information </h2>
{table_imageinfo}
</td>
</tr>
</table>
<table>
<tr>
<td>{table_dimensions}</td>
</tr>
</table>
"""

return '\n'.join([
html_style_header,
'<body>',
table_assembly,
'</body>',
'</html>'
])


ImageWrapper = _ImageWrapper

# INSTRUMENT AND ACQUISITION #
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