-
Frame Nr. 20
+
+
- + Frame Nr. 20
-
- 
+
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- 
+
+
-
- 
+
+
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- 
+
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+
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+
-
Frame Nr. 29
+
+
- + Frame Nr. 28
-
- 
+
+ 
-
- 
+
+ 
-
- 
+
+ 
-
- 
+
+ 
+
+
+
+
-
Frame Nr. 38
+
+
- + Frame Nr. 36
-
- 
+
+ 
-
- 
+
+ 
-
- 
+
+ 
-
- 
+
+ 
+
+
+
+
-
Frame Nr. 47
+
+
- + Frame Nr. 44
-
- 
+
+ 
-
- 
+
+ 
-
- 
+
+ 
-
- 
+
+ 
+
+
+
+
-
Frame Nr. 56
+
+
- + Frame Nr. 52
-
- 
+
+ 
-
- 
+
+ 
-
- 
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+ 
-
- 
+
+ 
+
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-
Frame Nr. 65
+
+
- + Frame Nr. 60
-
- 
+
+ 
-
- 
+
+ 
-
- 
+
+ 
-
- 
+
+ 
+
+
+
+
-
-wavelet transforms image stacks
-
- 0.1.1
-
-
-
- spyboat
-
- python $__tool_directory__/spyboat_cli.py --version
- $log
-
- ]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- save_preprocessed['selection'] == 'Yes'
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- @article{monke2020optimal,
- title={Optimal time frequency analysis for biological data-pyBOAT},
- author={M{\"o}nke, Gregor and Sorgenfrei, Frieda A and Schmal, Christoph and Granada, Adri{\'a}n E},
- journal={bioRxiv},
- year={2020},
- publisher={Cold Spring Harbor Laboratory}
-}
-
-
-
diff -r a4c6fcf2c456 -r d5a4180410c4 __pycache__/output_report.cpython-38.pyc
Binary file __pycache__/output_report.cpython-38.pyc has changed
diff -r a4c6fcf2c456 -r d5a4180410c4 output_report.py
--- a/output_report.py Thu Nov 26 16:40:47 2020 +0000
+++ b/output_report.py Sat Nov 28 18:50:09 2020 +0000
@@ -1,28 +1,24 @@
-''' Produces plots and a summary html 'headless' '''
+""" Produces plots and a summary html 'headless' """
+import logging
+import os
-import os
import matplotlib
-# headless plotting and disable latex
-matplotlib.use('Agg')
-matplotlib.rcParams['text.usetex'] = False
import matplotlib.pyplot as ppl
-
-import logging
-
import spyboat.plotting as spyplot
+ppl.switch_backend('Agg')
+matplotlib.rcParams["text.usetex"] = False
logger = logging.getLogger(__name__)
# figure resolution
-DPI=250
+DPI = 250
-def produce_snapshots(input_movie, results, frame, Wkwargs,
- img_path='.'):
- '''
- Takes the *input_movie* and the
- *results* dictionary from spyboat.processing.run_parallel
- and produces phase, period and amplitude snapshot png's.
+def produce_snapshots(input_movie, results, frame, Wkwargs, img_path="."):
+ """
+ Takes the *input_movie* and the *results* dictionary
+ from spyboat.processing.run_parallel and produces phase,
+ period and amplitude snapshot png's.
For the period snapshot also the period range is needed,
hence the analysis dictionary 'Wkwargs' also gets passed.
@@ -32,103 +28,111 @@
and the storage location in *img_path*.
These get picked up by 'create_html'
- '''
-
+ """
spyplot.input_snapshot(input_movie[frame])
fig = ppl.gcf()
- out_path = os.path.join(img_path, f'input_frame{frame}.png')
+ out_path = os.path.join(img_path, f"input_frame{frame}.png")
+ fig.savefig(out_path, dpi=DPI)
+ ppl.close(fig)
+
+ spyplot.phase_snapshot(results["phase"][frame])
+ fig = ppl.gcf()
+ out_path = os.path.join(img_path, f"phase_frame{frame}.png")
fig.savefig(out_path, dpi=DPI)
ppl.close(fig)
-
- spyplot.phase_snapshot(results['phase'][frame])
+
+ spyplot.period_snapshot(
+ results["period"][frame], Wkwargs["Tmin"],
+ Wkwargs["Tmax"], time_unit="a.u."
+ )
+
fig = ppl.gcf()
- out_path = os.path.join(img_path, f'phase_frame{frame}.png')
+ out_path = os.path.join(img_path, f"period_frame{frame}.png")
+ fig.savefig(out_path, dpi=DPI)
+ ppl.close(fig)
+
+ spyplot.amplitude_snapshot(results["amplitude"][frame])
+ fig = ppl.gcf()
+ out_path = os.path.join(img_path, f"amplitude_frame{frame}.png")
fig.savefig(out_path, dpi=DPI)
ppl.close(fig)
- spyplot.period_snapshot(results['period'][frame],
- Wkwargs['Tmin'],Wkwargs['Tmax'],
- time_unit = 'a.u.')
-
- fig = ppl.gcf()
- out_path = os.path.join(img_path, f'period_frame{frame}.png')
- fig.savefig(out_path, dpi=DPI)
- ppl.close(fig)
-
- spyplot.amplitude_snapshot(results['amplitude'][frame])
- fig = ppl.gcf()
- out_path = os.path.join(img_path, f'amplitude_frame{frame}.png')
- fig.savefig(out_path, dpi=DPI)
- ppl.close(fig)
-
- logger.info(f'Produced 4 snapshots for frame {frame}..')
+ logger.info(f"Produced 4 snapshots for frame {frame}..")
+
+
+def produce_distr_plots(results, Wkwargs, img_path="."):
+ """
+ Output file names are:
-def produce_distr_plots(results, Wkwargs, img_path='.'):
-
- '''
- Output file names are:
-
- period_distr.png, power_distr.png and phase_distr.png
- '''
+ period_distr.png, power_distr.png and phase_distr.png
+ """
- spyplot.period_distr_dynamics(results['period'], Wkwargs)
+ spyplot.period_distr_dynamics(results["period"], Wkwargs)
fig = ppl.gcf()
- out_path = os.path.join(img_path, f'period_distr.png')
+ out_path = os.path.join(img_path, "period_distr.png")
fig.savefig(out_path, dpi=DPI)
-
- spyplot.power_distr_dynamics(results['power'], Wkwargs)
+
+ spyplot.power_distr_dynamics(results["power"], Wkwargs)
fig = ppl.gcf()
- out_path = os.path.join(img_path, f'power_distr.png')
+ out_path = os.path.join(img_path, "power_distr.png")
fig.savefig(out_path, dpi=DPI)
- spyplot.phase_coherence_dynamics(results['phase'], Wkwargs)
+ spyplot.phase_coherence_dynamics(results["phase"], Wkwargs)
fig = ppl.gcf()
- out_path = os.path.join(img_path, f'phase_distr.png')
+ out_path = os.path.join(img_path, "phase_distr.png")
fig.savefig(out_path, dpi=DPI)
-
- logger.info(f'Produced 3 distribution plots..')
+
+ logger.info("Produced 3 distribution plots..")
+
-
-def create_html(frame_nums, html_fname='OutputReport.html'):
-
- '''
- The html generated assumes the respective png's
+def create_html(frame_nums, html_fname="OutputReport.html"):
+ """
+ The html generated assumes the respective png's
have been created with 'produce_snapshots' and 'produce_distr_plots'
and can be found at the cwd (that's how Galaxy works..)
- '''
+ """
# -- create a gallery for every frame in frame_nums --
-
- galleries = ''
+
+ galleries = ""
for frame_num in frame_nums:
- new_gal =f'''
-
Frame Nr. 74
+
+
diff -r a4c6fcf2c456 -r d5a4180410c4 SpyBOAT.xml
--- a/SpyBOAT.xml Thu Nov 26 16:40:47 2020 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,248 +0,0 @@
-+ Frame Nr. 68
-
- 
+
+ 
-
- 
+
+ 
-
- 
+
+ 
-
- 
+
+ 
+
+
+
+
- SpyBOAT Output Report
@@ -152,7 +156,7 @@
text-align: center;
/* border: 1px dashed rgba(4, 4, 4, 0.35); */
grid-template-columns: repeat(3,1fr);
- grid-template-rows: 20vw;
+ grid-template-rows: 20vw;
grid-gap: 0px;
column-gap: 0px
}}
@@ -186,7 +190,7 @@
+
@@ -237,13 +241,12 @@
- '''
+ """
- with open(html_fname, 'w') as OUT:
-
+ with open(html_fname, "w") as OUT:
OUT.write(html_string)
- logger.info(f'Created html report')
+ logger.info("Created html report")
return html_string
# for local testing
diff -r a4c6fcf2c456 -r d5a4180410c4 period_out.tif
Binary file period_out.tif has changed
diff -r a4c6fcf2c456 -r d5a4180410c4 phase_out.tif
Binary file phase_out.tif has changed
diff -r a4c6fcf2c456 -r d5a4180410c4 run_tests.sh
--- a/run_tests.sh Thu Nov 26 16:40:47 2020 +0000
+++ b/run_tests.sh Sat Nov 28 18:50:09 2020 +0000
@@ -4,7 +4,11 @@
INPUT_PATH='./test-data/test-movie.tif'
SCRIPT_PATH='.'
-python3 $SCRIPT_PATH/spyboat_cli.py --input_path $INPUT_PATH --phase_out phase_test-movie.tif --period_out period_test-movie.tif --power_out power_test-movie.tif --amplitude_out amplitude_test-movie.tif --dt 1 --Tmin 20 --Tmax 30 --nT 200 --ncpu 6 --masking dynamic --preprocessed_out preproc_two_sines.tif --gauss_sigma 2 --rescale 80 --Tcutoff 40 --masking static --mask_frame 10 --mask_thresh 300
+# set to galaxy defaults!!
+python3 $SCRIPT_PATH/spyboat_cli.py --input_path $INPUT_PATH --phase_out phase_out.tif --period_out period_out.tif --dt 1 --Tmin 20 --Tmax 30 --nT 150 --ncpu 6 --Tcutoff 40
+
+# additional paramters
+#--masking static --mask_frame 10 --mask_thresh 300 --rescale 80 --gauss_sigma 1
printf "\n"
# printf "\nError examples:\n"
diff -r a4c6fcf2c456 -r d5a4180410c4 spyboat.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/spyboat.xml Sat Nov 28 18:50:09 2020 +0000
@@ -0,0 +1,264 @@
+
+wavelet transforms image stacks
+
+ 0.1.1
+
+
+ spyboat
+
+ python '$__tool_directory__/spyboat_cli.py' --version
+ /dev/null &&
+ ## run tool
+ python '$__tool_directory__/spyboat_cli.py'
+ --input_path '$movie'
+ #if str($PreProc.gauss_sigma):
+ --gauss_sigma $PreProc.gauss_sigma
+ #end if
+ #if str($PreProc.rescale_factor):
+ --rescale $PreProc.rescale_factor
+ #end if
+
+ #if $masking.selection_mode == "create_static_mask":
+ --masking static
+ --mask_frame $masking.mask_frame
+ --mask_thresh $masking.mask_thresh
+ #else if $masking.selection_mode == "create_dynamic_mask":
+ --masking dynamic
+ --mask_thresh $masking.mask_thresh
+ #end if
+
+ --dt $wavana.dt
+ --Tmin $wavana.tmin
+ --Tmax $wavana.tmax
+ --nT $wavana.nt
+ #if str($wavana.tcutoff)
+ --Tcutoff $wavana.tcutoff
+ #end if
+ #if str($wavana.win_size):
+ --win_size $wavana.win_size
+ #end if
+
+ #if 'save_phase' in $outputs:
+ --phase_out '$phase_out'
+ #end if
+
+ #if 'save_period' in $outputs:
+ --period_out '$period_out'
+ #end if
+
+ #if 'save_power' in $outputs:
+ --power_out '$power_out'
+ #end if
+
+ #if 'save_amplitude' in $outputs:
+ --amplitude_out '$amplitude_out'
+ #end if
+
+ #if 'save_preprocessed' in $outputs:
+ --preprocessed_out '$preprocessed_out'
+ #end if
+
+ --html_fname '$html_out'
+ --report_img_path '$html_out.extra_files_path'
+
+ --ncpu "\${GALAXY_SLOTS:-8}"
+
+
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 'save_phase' in ouputs
+
+
+ 'save_period' in outputs
+
+
+ 'save_power' in outputs
+
+
+ 'save_amplitude' in outputs
+
+
+ 'save_preprocessed' in outputs
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1101/2020.04.29.067744
+
+
diff -r a4c6fcf2c456 -r d5a4180410c4 spyboat_cli.py
--- a/spyboat_cli.py Thu Nov 26 16:40:47 2020 +0000
+++ b/spyboat_cli.py Sat Nov 28 18:50:09 2020 +0000
@@ -1,15 +1,15 @@
#!/usr/bin/env python
-## Gets interfaced by Galaxy or can be used for bash scripting
+# Gets interfaced by Galaxy or can be used for bash scripting
import argparse
-import sys, os
import logging
+import os
+import sys
-from skimage import io
+import output_report
+import spyboat
from numpy import float32
-
-import spyboat
-import output_report
+from skimage import io
logging.basicConfig(level=logging.INFO, stream=sys.stdout, force=True)
logger = logging.getLogger('spyboat-cli')
@@ -20,12 +20,11 @@
# I/O
parser.add_argument('--input_path', help="Input movie location", required=True)
-parser.add_argument('--phase_out', help='Phase output file name', required=True)
-parser.add_argument('--period_out', help='Period output file name', required=True)
-parser.add_argument('--power_out', help='Power output file name', required=True)
-parser.add_argument('--amplitude_out', help='Amplitude output file name', required=True)
-parser.add_argument('--preprocessed_out', help="Preprocessed-input output file name, 'None'", required=False)
-
+parser.add_argument('--phase_out', help='Phase output file name', required=False)
+parser.add_argument('--period_out', help='Period output file name', required=False)
+parser.add_argument('--power_out', help='Power output file name', required=False)
+parser.add_argument('--amplitude_out', help='Amplitude output file name', required=False)
+parser.add_argument('--preprocessed_out', help="Preprocessed-input output file name", required=False)
# (Optional) Multiprocessing
@@ -33,10 +32,11 @@
required=False, type=int, default=1)
# Optional spatial downsampling
-parser.add_argument('--rescale', help='Rescale the image by a factor given in %%, None means no rescaling',
+parser.add_argument('--rescale_factor', help='Rescale the image by a factor given in %%, None means no rescaling',
required=False, type=int)
# Optional Gaussian smoothing
-parser.add_argument('--gauss_sigma', help='Gaussian smoothing parameter, None means no smoothing', required=False, type=float)
+parser.add_argument('--gauss_sigma', help='Gaussian smoothing parameter, None means no smoothing', required=False,
+ type=float)
# Wavelet Analysis Parameters
parser.add_argument('--dt', help='Sampling interval', required=True, type=float)
@@ -49,14 +49,15 @@
required=False, type=float)
# Optional masking
-parser.add_argument('--masking', help="Set to either 'dynamic', 'static' or 'None' which is the default", default='None', required=False, type=str)
+parser.add_argument('--masking', help="Set to either 'dynamic', 'static' or 'None' which is the default",
+ default='None', required=False, type=str)
parser.add_argument('--mask_frame',
help="The frame of the input movie to create a static mask from, needs masking set to 'static'",
required=False, type=int)
-
-parser.add_argument('--mask_thresh', help='The threshold of the mask, all pixels with less than this value get masked (if masking enabled).',
+parser.add_argument('--mask_thresh',
+ help='The threshold of the mask, all pixels with less than this value get masked (if masking enabled).',
required=False, type=float,
default=0)
@@ -64,7 +65,8 @@
parser.add_argument('--html_fname', help="Name of the html report.",
default='OutputReport.html', required=False, type=str)
-parser.add_argument('--report_img_path', help="For the html report, to be set in Galaxy. Without galaxy leave at cwd!", default='.', required=False, type=str)
+parser.add_argument('--report_img_path', help="For the html report, to be set in Galaxy. Without galaxy leave at cwd!",
+ default='.', required=False, type=str)
parser.add_argument('--version', action='version', version='0.1.0')
@@ -85,7 +87,7 @@
sys.exit(1)
# -------- Do (optional) spatial downsampling ---------------------------
-scale_factor = arguments.rescale
+scale_factor = arguments.rescale_factor
# defaults to None
if not scale_factor:
@@ -121,13 +123,13 @@
sys.exit(1)
else:
- logger.info(f'Creating static mask from frame {arguments.mask_frame} with threshold {arguments.mask_thresh}')
+ logger.info(f'Creating static mask from frame {arguments.mask_frame} with threshold {arguments.mask_thresh}')
mask = spyboat.create_static_mask(movie, arguments.mask_frame,
- arguments.mask_thresh)
+ arguments.mask_thresh)
elif arguments.masking == 'dynamic':
logger.info(f'Creating dynamic mask with threshold {arguments.mask_thresh}')
mask = spyboat.create_dynamic_mask(movie, arguments.mask_thresh)
-
+
else:
logger.info('No masking requested..')
@@ -135,11 +137,11 @@
Wkwargs = {'dt': arguments.dt,
'Tmin': arguments.Tmin,
- 'Tmax': arguments.Tmax,
+ 'Tmax': arguments.Tmax,
'nT': arguments.nT,
- 'T_c' : arguments.Tcutoff, # defaults to None
- 'win_size' : arguments.win_size # defaults to None
-}
+ 'T_c': arguments.Tcutoff, # defaults to None
+ 'win_size': arguments.win_size # defaults to None
+ }
# --- start parallel processing ---
@@ -161,51 +163,55 @@
if arguments.report_img_path != '.':
logger.info(f'Creating report directory {arguments.report_img_path}')
- os.mkdir(arguments.report_img_path)
+ os.mkdir(arguments.report_img_path)
- # 4 snapshots each
+ # 4 snapshots each
Nsnap = 7
NFrames = movie.shape[0]
# show only frames at least one Tmin
# away from the edge (-effects)
- start_frame = int(Wkwargs['Tmin']/Wkwargs['dt'])
-
- if (start_frame > NFrames//2):
+ start_frame = int(Wkwargs['Tmin'] / Wkwargs['dt'])
+
+ if (start_frame > NFrames // 2):
logger.warning("Smallest period already is larger than half the observation time!")
# set to 0 in this case
start_frame = 0
-
- frame_increment = int( (NFrames - 2*start_frame) / Nsnap)
+
+ frame_increment = int((NFrames - 2 * start_frame) / Nsnap)
snapshot_frames = range(start_frame, NFrames - start_frame, frame_increment)
- for snapshot_frame in snapshot_frames:
+ for snapshot_frame in snapshot_frames:
output_report.produce_snapshots(movie, results, snapshot_frame, Wkwargs, img_path=arguments.report_img_path)
-
+
output_report.produce_distr_plots(results, Wkwargs, img_path=arguments.report_img_path)
-
+
output_report.create_html(snapshot_frames, arguments.html_fname)
-
+
except FileExistsError as e:
logger.critical(f"Could not create html report directory: {repr(e)}")
-
# --- save out result movies ---
-# save phase movie
-io.imsave(arguments.phase_out, results['phase'], plugin="tifffile")
-logger.info(f'Written {arguments.phase_out}')
-# save period movie
-io.imsave(arguments.period_out, results['period'], plugin="tifffile")
-logger.info(f'Written {arguments.period_out}')
-# save power movie
-io.imsave(arguments.power_out, results['power'], plugin="tifffile")
-logger.info(f'Written {arguments.power_out}')
-# save amplitude movie
-io.imsave(arguments.amplitude_out, results['amplitude'], plugin="tifffile")
-logger.info(f'Written {arguments.amplitude_out}')
+# None means output is filtered from galaxy settings
+if arguments.phase_out is not None:
+ # save phase movie
+ io.imsave(arguments.phase_out, results['phase'], plugin="tifffile")
+ logger.info(f'Written phase to {arguments.phase_out}')
+if arguments.period_out is not None:
+ # save period movie
+ io.imsave(arguments.period_out, results['period'], plugin="tifffile")
+ logger.info(f'Written period to {arguments.period_out}')
+if arguments.power_out is not None:
+ # save power movie
+ io.imsave(arguments.power_out, results['power'], plugin="tifffile")
+ logger.info(f'Written power to {arguments.power_out}')
+if arguments.amplitude_out is not None:
+ # save amplitude movie
+ io.imsave(arguments.amplitude_out, results['amplitude'], plugin="tifffile")
+ logger.info(f'Written amplitude to {arguments.amplitude_out}')
# save out the probably pre-processed (scaled and blurred) input movie for
# direct comparison to results and coordinate mapping etc.
-if arguments.preprocessed_out:
- io.imsave(arguments.preprocessed_out, movie, plugin='tifffile')
- logger.info(f'Written {arguments.preprocessed_out}')
+if arguments.preprocessed_out is not None:
+ io.imsave(arguments.preprocessed_out, movie.astype(float32), plugin='tifffile')
+ logger.info(f'Written preprocessed to {arguments.preprocessed_out}')
diff -r a4c6fcf2c456 -r d5a4180410c4 test-data/output1.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output1.html Sat Nov 28 18:50:09 2020 +0000
@@ -0,0 +1,334 @@
+
+
+
+ SpyBOAT Output Report
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff -r a4c6fcf2c456 -r d5a4180410c4 test-data/phase_out.tif
Binary file test-data/phase_out.tif has changed
Frame Nr. {frame_num}
+ new_gal = f""" +
+
- '''
+ """
galleries += new_gal
-
- html_string =f'''
+
+ html_string = f"""
+ Frame Nr. {frame_num}
-
- 
+
+
-
- 
+
+
-
- 
+
+
-
- 
+
+
+
+
+
+
SpyBOAT Results Report
-+
Distribution Dynamics
SpyBOAT Results Report
++
Distribution Dynamics
+
+
+ 
+
+
+
+ 
+
+
+
+ 
+
+
+
+
+
+
+
+ Output Movie Snapshots
+ + +
+
+
+
+
+
+
+
+
+
+ + Frame Nr. 20
+ +
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ + Frame Nr. 28
+ +
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+ + Frame Nr. 36
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+ + Frame Nr. 52
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