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Group layer elements (#45)
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Closes #42

- Elements from a single layer are grouped in `<g>`
- Change layer-to-xml functions to return elements rather than lists
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@jni
jni authored Jun 20, 2024
1 parent f1e125c commit dfd90a5
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Showing 3 changed files with 36 additions and 38 deletions.
2 changes: 1 addition & 1 deletion napari_svg/_tests/test_write_points_with_attributes-expected.svg
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24 changes: 12 additions & 12 deletions napari_svg/hook_implementations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,8 +80,8 @@ def writer(path, layer_data):
full_extrema = None
for ld in layer_data:
function_string = ld[2] + '_to_xml(ld[0], ld[1])'
xml_list, extrema = eval(function_string)
full_xml_list += xml_list
layer_xml, extrema = eval(function_string)
full_xml_list.append(layer_xml)
if full_extrema is None:
full_extrema = extrema
else:
Expand Down Expand Up @@ -140,10 +140,10 @@ def napari_write_image(path, data, meta):
return None

# Generate xml list and data extrema
xml_list, extrema = image_to_xml(data, meta)
layer_xml, extrema = image_to_xml(data, meta)

# Generate svg string
svg = xml_to_svg(xml_list, extrema=extrema)
svg = xml_to_svg(layer_xml, extrema=extrema)

# Write svg string
with open(path, 'w') as file:
Expand Down Expand Up @@ -183,10 +183,10 @@ def napari_write_labels(path, data, meta):
return None

# Generate xml list and data extrema
xml_list, extrema = labels_to_xml(data, meta)
layer_xml, extrema = labels_to_xml(data, meta)

# Generate svg string
svg = xml_to_svg(xml_list, extrema=extrema)
svg = xml_to_svg([layer_xml], extrema=extrema)

# Write svg string
with open(path, 'w') as file:
Expand Down Expand Up @@ -225,10 +225,10 @@ def napari_write_points(path, data, meta):
return None

# Generate xml list and data extrema
xml_list, extrema = points_to_xml(data, meta)
layer_xml, extrema = points_to_xml(data, meta)

# Generate svg string
svg = xml_to_svg(xml_list, extrema=extrema)
svg = xml_to_svg([layer_xml], extrema=extrema)

# Write svg string
with open(path, 'w') as file:
Expand Down Expand Up @@ -266,10 +266,10 @@ def napari_write_shapes(path, data, meta):
return None

# Generate xml list and data extrema
xml_list, extrema = shapes_to_xml(data, meta)
layer_xml, extrema = shapes_to_xml(data, meta)

# Generate svg string
svg = xml_to_svg(xml_list, extrema=extrema)
svg = xml_to_svg([layer_xml], extrema=extrema)

# Write svg string
with open(path, 'w') as file:
Expand Down Expand Up @@ -307,10 +307,10 @@ def napari_write_vectors(path, data, meta):
return None

# Generate xml list and data extrema
xml_list, extrema = vectors_to_xml(data, meta)
layer_xml, extrema = vectors_to_xml(data, meta)

# Generate svg string
svg = xml_to_svg(xml_list, extrema=extrema)
svg = xml_to_svg([layer_xml], extrema=extrema)

# Write svg string
with open(path, 'w') as file:
Expand Down
48 changes: 23 additions & 25 deletions napari_svg/layer_to_xml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -136,8 +136,8 @@ def image_to_xml(data, meta):
Returns
-------
xml_list : list of xml.etree.ElementTree.Element
List of a single xml element specifying the image as a png according to
layer_xml : xml.etree.ElementTree.Element
Single xml element specifying the image as a png according to
the svg specification.
extrema : array (2, 2)
Extrema of data, specified as a minumum then maximum of the (x, y)
Expand Down Expand Up @@ -208,17 +208,16 @@ def image_to_xml(data, meta):

transform = layer_transforms_to_xml_string(meta)

xml = Element(
layer_xml = Element(
'image',
width=width,
height=height,
opacity=str(opacity),
transform=transform,
**props,
)
xml_list = [xml]

return xml_list, extrema
return layer_xml, extrema


def extrema_points(data, meta):
Expand Down Expand Up @@ -249,9 +248,9 @@ def points_to_xml(data, meta):
Returns
-------
xml_list : list of xml.etree.ElementTree.Element
List of xml elements defining each point according to the
svg specification
layer_xml : xml.etree.ElementTree.Element
XML group element containing each point according to the
svg specification.
extrema : array (2, 2)
Extrema of data, specified as a minumum then maximum of the (x, y)
coordinates.
Expand Down Expand Up @@ -307,8 +306,8 @@ def points_to_xml(data, meta):
stroke_width *= size

transform = layer_transforms_to_xml_string(meta)
layer_xml = Element('g', transform=transform)

xml_list = []
for p, s, fc, sc, sw in zip(points, size, face_color, stroke_color, stroke_width):
cx = str(p[1])
cy = str(p[0])
Expand All @@ -326,12 +325,11 @@ def points_to_xml(data, meta):
cx=cx, cy=cy, r=r,
stroke=stroke,
fill=fill,
transform=transform,
**props,
)
xml_list.append(element)
layer_xml.append(element)

return xml_list, extrema
return layer_xml, extrema


def extrema_shapes(shapes_data, meta):
Expand All @@ -355,8 +353,8 @@ def shapes_to_xml(data, meta):
Returns
-------
xml_list : list of xml.etree.ElementTree.Element
List of xml elements defining each shapes according to the
layer_xml : xml.etree.ElementTree.Element
XML group element containing each shape according to the
svg specification
extrema : array (2, 2)
Extrema of data, specified as a minumum then maximum of the (x, y)
Expand Down Expand Up @@ -404,13 +402,13 @@ def shapes_to_xml(data, meta):
extrema = np.full((2, 2), np.nan)

transform = layer_transforms_to_xml_string(meta)
layer_xml = Element('g', transform=transform)
raw_xml_list = []
zipped = zip(shapes, shape_type, face_color, edge_color, edge_width)
for s, st, fc, ec, ew in zipped:
props = {
'stroke-width': str(ew),
'opacity': str(opacity),
'transform': transform,
}
fc_int = (255 * fc).astype(int)
props['fill'] = f'rgb{tuple(map(int, fc_int[:3]))}'
Expand All @@ -421,9 +419,9 @@ def shapes_to_xml(data, meta):
raw_xml_list.append(element)

# reorder according to z-index
z_order = np.argsort(z_index)
xml_list = [raw_xml_list[i] for i in z_order]
return xml_list, extrema
for i in np.argsort(z_index):
layer_xml.append(raw_xml_list[i])
return layer_xml, extrema


def extrema_vectors(vectors, meta):
Expand Down Expand Up @@ -455,8 +453,8 @@ def vectors_to_xml(data, meta):
Returns
-------
xml_list : list of xml.etree.ElementTree.Element
List of xml elements defining each vector as a line according to the
layer_xml : xml.etree.ElementTree.Element
XML group element containing each vector as a line according to the
svg specification
extrema : array (2, 2)
Extrema of data, specified as a minumum then maximum of the (x, y)
Expand Down Expand Up @@ -494,13 +492,12 @@ def vectors_to_xml(data, meta):
extrema = extrema_vectors(vectors, meta)

transform = layer_transforms_to_xml_string(meta)
layer_xml = Element('g', transform=transform)

props = {
'stroke-width': str(edge_width),
'opacity': str(opacity),
'transform': transform,
}

xml_list = []
for v, ec in zip(vectors, edge_color):
x1 = str(v[0, -2])
y1 = str(v[0, -1])
Expand All @@ -510,6 +507,7 @@ def vectors_to_xml(data, meta):
stroke = f'rgb{tuple(map(int, ec_int[:3]))}'
props['stroke'] = stroke
element = Element('line', x1=y1, y1=x1, x2=y2, y2=x2, **props)
xml_list.append(element)
layer_xml.append(element)


return xml_list, extrema
return layer_xml, extrema

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