import h5py
import matplotlib.pyplot as plt
import streamlit as st
from IPython.display import display
from solidipes.viewers import backends as viewer_backends
from solidipes.viewers.viewer import Viewer
from streamlit_tree_select import tree_select
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def scan_hdf5_recursively(f):
res = {"label": f.name}
res["value"] = f.name
if isinstance(f, h5py.Dataset):
return res, [f.name]
res["children"] = []
labs = [f.name]
for k, v in f.items():
_nd, lab = scan_hdf5_recursively(v)
res["children"].append(_nd)
labs += lab
return res, labs
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class HDF5(Viewer):
"""Viewer for HDf5"""
def __init__(self, data=None):
#: Image to display
self.datasets = None
super().__init__(data)
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def add(self, data_container):
"""Replace the viewer's hdf5"""
self.check_data_compatibility(data_container)
self.datasets = data_container.datasets
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def show(self):
if viewer_backends.current_backend == "jupyter notebook":
display(self.datasets)
elif viewer_backends.current_backend == "streamlit":
col1, col2 = st.columns(2)
nodes, labels = scan_hdf5_recursively(self.datasets)
nodes = [nodes]
# st.write(nodes)
with col1:
return_select = tree_select(
nodes,
check_model="leaf",
no_cascade=True,
expand_on_click=True,
only_leaf_checkboxes=True,
expanded=labels,
)
with col2:
for e in return_select["checked"]:
d = self.datasets[e]
st.markdown(f"### {e} ({type(d).__name__})")
try:
st.markdown(f"Shape: {d.shape}")
except Exception:
pass
if len(d.shape) == 2 and d.shape[0] > 30 and d.shape[1] > 30:
div = [d.shape[i] // 2000 for i in range(len(d.shape))]
fig, ax = plt.subplots()
filtered = d[:: div[0], :: div[1]]
ax.imshow(filtered)
st.pyplot(fig)
elif len(d.shape) == 1:
div = d.shape[0] // 2000
if div == 0:
div = 1
fig, ax = plt.subplots()
filtered = d[::div]
ax.plot(filtered, "-o")
ax.set_xlabel("index")
st.pyplot(fig)
else:
slices = [slice(0, min(20, d.shape[i]), 1) for i in range(len(d.shape))]
st.dataframe(d.__getitem__(*slices))
else: # python
print(self.datasets)