Skip to content

Optionally use Zopfli on the trace data #294

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Optionally use Zopfli on the trace data #294

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
d9a47a9
Fix ROI Trace parameter documentation
jakirkham Nov 27, 2018
4fb351d
Require `zopfli`
jakirkham Nov 27, 2018
81e0223
Provide an option to set zlib compression level
jakirkham Nov 27, 2018
17cd7eb
Provide option to use Zopfli
jakirkham Nov 27, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
26 changes: 17 additions & 9 deletions nanshe_ipython.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1671,6 +1671,9 @@
"import mmap\n",
"import textwrap\n",
"\n",
"import zopfli\n",
"import zopfli.gzip\n",
"\n",
"import numpy\n",
"import numpy as np\n",
"\n",
Expand Down Expand Up @@ -1727,9 +1730,9 @@
"* `block_size` (`int`): size of each point on any dimension in the image in terms of pixels.\n",
"* `roi_alpha` (`float`): transparency of the ROIs in a range of [0.0, 1.0].\n",
"* `roi_border_width` (`int`): width of the line border on each ROI.\n",
"\n",
"<br>\n",
"* `trace_plot_width` (`int`): width of the trace plot."
"* `trace_plot_width` (`int`): width of the trace plot.\n",
"* `compresslevel` (`int`): compression level to use with zlib for trace data [0, 9].\n",
"* `use_zopfli` (`bool`): whether to use Zopfli or zlib."
]
},
{
Expand All @@ -1743,6 +1746,8 @@
"roi_alpha = 0.3\n",
"roi_border_width = 3\n",
"trace_plot_width = 500\n",
"compresslevel = 6\n",
"use_zopfli = False\n",
"\n",
"\n",
"bio.curdoc().clear()\n",
Expand Down Expand Up @@ -1821,18 +1826,21 @@
" plot_projs.append(plot_std)\n",
"\n",
"\n",
"def gzip_compress(data, compresslevel=6):\n",
" compressed = io.BytesIO()\n",
" with gzip.GzipFile(fileobj=compressed, mode=\"wb\", compresslevel=compresslevel) as compressor:\n",
" compressor.write(data)\n",
" return compressed.getvalue()\n",
"def gzip_compress(data, compresslevel=6, use_zopfli=False):\n",
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

May want to toy with how these are exposed to the user.

" if use_zopfli:\n",
" return zopfli.gzip.compress(data, gzip_mode=compresslevel)\n",
" else:\n",
" compressed = io.BytesIO()\n",
" with gzip.GzipFile(fileobj=compressed, mode=\"wb\", compresslevel=compresslevel) as compressor:\n",
" compressor.write(data)\n",
" return compressed.getvalue()\n",
"\n",
"\n",
"all_tr_dtype_srcs = ColumnDataSource(data=dict(traces_dtype=traces.dtype.type(0)[None]))\n",
"all_tr_shape_srcs = ColumnDataSource(data=dict(traces_shape=traces.shape))\n",
"all_tr_srcs = ColumnDataSource(data=dict(\n",
" traces=numpy.frombuffer(\n",
" gzip_compress(traces.tobytes()),\n",
" gzip_compress(traces.tobytes(), compresslevel=compresslevel, use_zopfli=use_zopfli),\n",
" dtype=np.uint8\n",
" )\n",
"))\n",
Expand Down
1 change: 1 addition & 0 deletions nanshe_workflow.recipe/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@ requirements:
- xnumpy
- yail
- zarr
- zopfli

about:
home: {{ data.get("url") }}
Expand Down