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made zip structure closer to .saenopy file
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@rgerum
rgerum committed Mar 19, 2024
1 parent 17d356d commit 2739b46
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Showing 3 changed files with 63 additions and 29 deletions.
55 changes: 40 additions & 15 deletions docs/source/_static/js/3d_viewer.mjs
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,13 @@ const zip_entries = {}
async function get_file_from_zip(url, filename, return_type="blob") {
if(zip_entries[url] === undefined) {
async function get_entries(url) {
const zipReader = new ZipReader(new BlobReader(await (await fetch(url)).blob()));
let zipReader;
if(typeof url === "string") {
zipReader = new ZipReader(new BlobReader(await (await fetch(url)).blob()));
}
else {
zipReader = new ZipReader(new BlobReader(url));
}
const entries = await zipReader.getEntries();
const entry_map = {}
for (let entry of entries) {
Expand Down Expand Up @@ -393,7 +399,7 @@ async function add_image(scene, params) {

const textures = [];
for (let i = 0; i < params.data.stacks.z_slices_count; i++) {
textures.push(get_file_from_zip(params.data.path, "0/stack/" + params.data.stacks.channels[0] + "/" + pad_zero(i, 3) + ".jpg", "texture"));
textures.push(get_file_from_zip(params.data.path, "stacks/0/" + params.data.stacks.channels[0] + "/" + pad_zero(i, 3) + ".jpg", "texture"));
textures[i].then((v) => {textures[i] = v})
}

Expand Down Expand Up @@ -461,24 +467,34 @@ async function add_test(scene, params) {
needs_update = true;
if (params.field !== "none") {
try {
nodes = await loadNpy(await get_file_from_zip(params.data.path, "0/" + params.data.fields[params.field].nodes, "blob"));
vectors = await loadNpy(await get_file_from_zip(params.data.path, "0/" + params.data.fields[params.field].vectors, "blob"));
nodes = await loadNpy(await get_file_from_zip(params.data.path, params.data.fields[params.field].nodes, "blob"));
vectors = await loadNpy(await get_file_from_zip(params.data.path, params.data.fields[params.field].vectors, "blob"));
} catch (e) {}
}

if (!nodes || !vectors) {
} else {
for (let i = 0; i < nodes.length; i++) {
const position = convert_pos(
nodes[i * 3],
nodes[i * 3 + 1],
nodes[i * 3 + 2],
);
const orientationVector = convert_vec(
vectors[i * 3],
vectors[i * 3 + 1],
vectors[i * 3 + 2],
);
for (let i = 0; i < nodes.header.shape[0]; i++) {
const position = nodes.header.fortran_order ?
convert_pos(
nodes[i],
nodes[i + nodes.header.shape[0]],
nodes[i + nodes.header.shape[0]*2],
) : convert_pos(
nodes[i * nodes.header.shape[1]],
nodes[i * nodes.header.shape[1] + 1],
nodes[i * nodes.header.shape[1] + 2],
);
const orientationVector = vectors.header.fortran_order ?
convert_vec(
vectors[i],
vectors[i + vectors.header.shape[0]],
vectors[i + vectors.header.shape[0]*2],
) : convert_vec(
vectors[i * vectors.header.shape[1]],
vectors[i * vectors.header.shape[1] + 1],
vectors[i * vectors.header.shape[1] + 2],
);
const target = position.clone().add(orientationVector);
const scaleValue = orientationVector.length();
if (scaleValue > max_length) {
Expand Down Expand Up @@ -606,6 +622,15 @@ export async function init(initial_params) {
extent: [0, 1, 0, 1, 0, 1],
...initial_params,
};
params.data = {
"fields": {
"measured deformations": {"nodes": "mesh_piv/0/nodes.npy", "vectors": "mesh_piv/0/displacements_measured.npy", "unit": "\u00b5m", "factor": 1000000.0},
"target deformations": {"nodes": "solvers/0/mesh/nodes.npy", "vectors": "solvers/0/mesh/displacements_target.npy", "unit": "\u00b5m", "factor": 1000000.0},
"fitted deformations": {"nodes": "solvers/0/mesh/nodes.npy", "vectors": "solvers/0/mesh/displacements.npy", "unit": "\u00b5m", "factor": 1000000.0},
"fitted forces": {"nodes": "solvers/0/mesh/nodes.npy", "vectors": "solvers/0/mesh/forces.npy", "unit": "nN", "factor": 1000000000.0}
},
...params.data
}

if(initial_params.dom_node) {
initial_params.dom_node.style.position = "relative";
Expand Down
1 change: 1 addition & 0 deletions docs/source/_static/js/load_numpy.js
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Original file line number Diff line number Diff line change
Expand Up @@ -40,5 +40,6 @@ export async function loadNpy(url) {
} else {
throw new Error("Unsupported dtype. Only Uint8 is supported. Got" + dtype);
}
data.header = header;
return data;
}
36 changes: 22 additions & 14 deletions saenopy/export_html.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,19 +33,23 @@ def export_html(result: saenopy.Result, path, zip_filename="data.zip", stack_qua

path_data = "0/"
def save(path, data, dtype):
new_data = np.zeros(data.shape, dtype=dtype)
new_data[:] = data
print(new_data.strides, new_data.shape)
#new_data = np.zeros(data.shape, dtype=dtype)
#new_data[:] = data
#print(new_data.strides, new_data.shape)

image_file = BytesIO()
np.save(image_file, new_data)
np.save(image_file, np.asarray(data).astype(dtype))
zipFp.writestr(path, image_file.getvalue())

data = {}
mesh = result.solvers[0].mesh
piv = result.mesh_piv[0]
save(path_data + "nodes_piv.npy", piv.nodes, np.float32)
save(path_data + "displacements_piv.npy", piv.displacements_measured, np.float32)

path_data = "mesh_piv/0/"
save(path_data + "nodes.npy", piv.nodes, np.float32)
save(path_data + "displacements_measured.npy", piv.displacements_measured, np.float32)

path_data = "solvers/0/mesh/"
save(path_data + "nodes.npy", mesh.nodes, np.float32)
save(path_data + "displacements_target.npy", mesh.displacements_target, np.float32)
save(path_data + "displacements.npy", mesh.displacements, np.float32)
Expand All @@ -67,13 +71,15 @@ def save(path, data, dtype):
if stack_downsample > 1:
im = im.resize((im.width//stack_downsample, im.height//stack_downsample), Image.Resampling.LANCZOS)
im.save(image_file, 'JPEG', quality=stack_quality)
zipFp.writestr(f"0/stack/0/{z//stack_downsample_z:03d}.jpg", image_file.getvalue())
zipFp.writestr(f"stacks/0/0/{z//stack_downsample_z:03d}.jpg", image_file.getvalue())
z_count += 1
voxel_size = result.get_data_structure()["voxel_size"]
voxel_size[2] = voxel_size[2] * stack_downsample_z

save("stacks/0/voxel_size.npy", voxel_size, np.float32)

im_shape = [int(x) for x in result.get_data_structure()["im_shape"]]
im_shape[2] = im_shape[2]//stack_downsample_z
voxel_size = result.get_data_structure()["voxel_size"]
voxel_size[2] = voxel_size[2] * stack_downsample_z

data["path"] = zip_filename

Expand All @@ -83,12 +89,14 @@ def save(path, data, dtype):
"im_shape": tuple(im_shape),
"voxel_size": tuple(voxel_size),
}
"""
data["fields"] = {
"measured deformations": {"nodes": "nodes_piv.npy", "vectors": "displacements_piv.npy", "unit": "µm", "factor": 1e6},
"target deformations": {"nodes": "nodes.npy", "vectors": "displacements_target.npy", "unit": "µm", "factor": 1e6},
"fitted deformations": {"nodes": "nodes.npy", "vectors": "displacements.npy", "unit": "µm", "factor": 1e6},
"fitted forces": {"nodes": "nodes.npy", "vectors": "forces.npy", "unit": "nN", "factor": 1e9},
"measured deformations": {"nodes": "mesh_piv/0/nodes.npy", "vectors": "mesh_piv/0/displacements_measured.npy", "unit": "µm", "factor": 1e6},
"target deformations": {"nodes": "solvers/0/mesh/nodes.npy", "vectors": "solvers/0/mesh/displacements_target.npy", "unit": "µm", "factor": 1e6},
"fitted deformations": {"nodes": "solvers/0/mesh/nodes.npy", "vectors": "solvers/0/mesh/displacements.npy", "unit": "µm", "factor": 1e6},
"fitted forces": {"nodes": "solvers/0/mesh/nodes.npy", "vectors": "solvers/0/mesh/forces.npy", "unit": "nN", "factor": 1e9},
}
"""
data["time_point_count"] = result.get_data_structure()["time_point_count"]

print(data)
Expand All @@ -115,7 +123,7 @@ def save(path, data, dtype):
"imports": {
"three": "https://unpkg.com/three@v0.158.0/build/three.module.js",
"three/addons/": "https://unpkg.com/three@v0.158.0/examples/jsm/",
"3d_viewer": "https://saenopy.readthedocs.io/en/latest/_static/js/3d_viewer.mjs"
"3d_viewer": "./3d_viewer.mjs"
}
}
</script>
Expand Down

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