def mrcnn():
summary_image = np.load(
'/home/nel/data/voltage_data/volpy_paper/memory/summary.npz'
)['arr_0']
config = neurons.NeuronsConfig()
class InferenceConfig(config.__class__):
# Run detection on one image at a time
GPU_COUNT = 1
IMAGES_PER_GPU = 1
DETECTION_MIN_CONFIDENCE = 0.7
IMAGE_RESIZE_MODE = "pad64"
IMAGE_MAX_DIM = 512
RPN_NMS_THRESHOLD = 0.7
POST_NMS_ROIS_INFERENCE = 1000
config = InferenceConfig()
config.display()
model_dir = os.path.join(caiman_datadir(), 'model')
DEVICE = "/cpu:0" # /cpu:0 or /gpu:0
with tf.device(DEVICE):
model = modellib.MaskRCNN(mode="inference",
model_dir=model_dir,
config=config)
weights_path = download_model('mask_rcnn')
model.load_weights(weights_path, by_name=True)
results = model.detect([summary_image], verbose=1)
r = results[0]
ROIs = r['masks'].transpose([2, 0, 1])
return ROIs
def mrcnn_inference(img, weights_path, display_result=True):
""" Mask R-CNN inference in VolPy
Args:
img: 2-D array
summary images for detection
weights_path: str
path for Mask R-CNN weight
display_result: boolean
if True, the function will plot the result of inference
Return:
ROIs: 3-D array
region of interests
(# of components * # of pixels in x dim * # of pixels in y dim)
"""
from caiman.source_extraction.volpy.mrcnn import visualize, neurons
import caiman.source_extraction.volpy.mrcnn.model as modellib
config = neurons.NeuronsConfig()
class InferenceConfig(config.__class__):
# Run detection on one img at a time
GPU_COUNT = 1
IMAGES_PER_GPU = 1
DETECTION_MIN_CONFIDENCE = 0.7
IMAGE_RESIZE_MODE = "pad64"
IMAGE_MAX_DIM = 512
RPN_NMS_THRESHOLD = 0.7
POST_NMS_ROIS_INFERENCE = 1000
config = InferenceConfig()
config.display()
model_dir = os.path.join(caiman_datadir(), 'model')
DEVICE = "/cpu:0" # /cpu:0 or /gpu:0
with tf.device(DEVICE):
model = modellib.MaskRCNN(mode="inference",
model_dir=model_dir,
config=config)
model.load_weights(weights_path, by_name=True)
results = model.detect([img], verbose=1)
r = results[0]
ROIs = r['masks'].transpose([2, 0, 1])
if display_result:
_, ax = plt.subplots(1, 1, figsize=(16, 16))
visualize.display_instances(img,
r['rois'],
r['masks'],
r['class_ids'], ['BG', 'neurons'],
r['scores'],
ax=ax,
title="Predictions")
return ROIs
def test_computational_performance(fnames, path_ROIs, n_processes):
import os
import cv2
import glob
import logging
import matplotlib.pyplot as plt
import numpy as np
import tensorflow as tf
import h5py
from time import time
try:
cv2.setNumThreads(0)
except:
pass
try:
if __IPYTHON__:
# this is used for debugging purposes only. allows to reload classes
# when changed
get_ipython().magic('load_ext autoreload')
get_ipython().magic('autoreload 2')
except NameError:
pass
import caiman as cm
from caiman.motion_correction import MotionCorrect
from caiman.utils.utils import download_demo, download_model
from caiman.source_extraction.volpy.volparams import volparams
from caiman.source_extraction.volpy.volpy import VOLPY
from caiman.source_extraction.volpy.mrcnn import visualize, neurons
import caiman.source_extraction.volpy.mrcnn.model as modellib
from caiman.paths import caiman_datadir
from caiman.summary_images import local_correlations_movie_offline
from caiman.summary_images import mean_image
from caiman.source_extraction.volpy.utils import quick_annotation
from multiprocessing import Pool
time_start = time()
print('Start MOTION CORRECTION')
# %% Load demo movie and ROIs
fnames = fnames
path_ROIs = path_ROIs
#%% dataset dependent parameters
# dataset dependent parameters
fr = 400 # sample rate of the movie
# motion correction parameters
pw_rigid = False # flag for pw-rigid motion correction
gSig_filt = (3, 3) # size of filter, in general gSig (see below),
# change this one if algorithm does not work
max_shifts = (5, 5) # maximum allowed rigid shift
strides = (
48, 48
) # start a new patch for pw-rigid motion correction every x pixels
overlaps = (24, 24
) # overlap between pathes (size of patch strides+overlaps)
max_deviation_rigid = 3 # maximum deviation allowed for patch with respect to rigid shifts
border_nan = 'copy'
opts_dict = {
'fnames': fnames,
'fr': fr,
'pw_rigid': pw_rigid,
'max_shifts': max_shifts,
'gSig_filt': gSig_filt,
'strides': strides,
'overlaps': overlaps,
'max_deviation_rigid': max_deviation_rigid,
'border_nan': border_nan
}
opts = volparams(params_dict=opts_dict)
# %% start a cluster for parallel processing
dview = Pool(n_processes)
#dview = None
# %%% MOTION CORRECTION
# first we create a motion correction object with the specified parameters
mc = MotionCorrect(fnames, dview=dview, **opts.get_group('motion'))
# Run correction
mc.motion_correct(save_movie=True)
time_mc = time() - time_start
print(time_mc)
print('START MEMORY MAPPING')
# %% restart cluster to clean up memory
dview.terminate()
dview = Pool(n_processes)
# %% MEMORY MAPPING
border_to_0 = 0 if mc.border_nan == 'copy' else mc.border_to_0
# you can include the boundaries of the FOV if you used the 'copy' option
# during motion correction, although be careful about the components near
# the boundaries
# memory map the file in order 'C'
fname_new = cm.save_memmap_join(mc.mmap_file,
base_name='memmap_',
add_to_mov=border_to_0,
dview=dview,
n_chunks=1000) # exclude border
time_mmap = time() - time_start - time_mc
print('Start Segmentation')
# %% SEGMENTATION
# create summary images
img = mean_image(mc.mmap_file[0], window=1000, dview=dview)
img = (img - np.mean(img)) / np.std(img)
Cn = local_correlations_movie_offline(mc.mmap_file[0],
fr=fr,
window=1500,
stride=1500,
winSize_baseline=400,
remove_baseline=True,
dview=dview).max(axis=0)
img_corr = (Cn - np.mean(Cn)) / np.std(Cn)
summary_image = np.stack([img, img, img_corr], axis=2).astype(np.float32)
#%% three methods for segmentation
methods_list = [
'manual_annotation', # manual annotation needs user to prepare annotated datasets same format as demo ROIs
'quick_annotation', # quick annotation annotates data with simple interface in python
'maskrcnn'
] # maskrcnn is a convolutional network trained for finding neurons using summary images
method = methods_list[0]
if method == 'manual_annotation':
with h5py.File(path_ROIs, 'r') as fl:
ROIs = fl['mov'][()] # load ROIs
elif method == 'quick_annotation':
ROIs = quick_annotation(img_corr, min_radius=4, max_radius=10)
elif method == 'maskrcnn':
config = neurons.NeuronsConfig()
class InferenceConfig(config.__class__):
# Run detection on one image at a time
GPU_COUNT = 1
IMAGES_PER_GPU = 1
DETECTION_MIN_CONFIDENCE = 0.7
IMAGE_RESIZE_MODE = "pad64"
IMAGE_MAX_DIM = 512
RPN_NMS_THRESHOLD = 0.7
POST_NMS_ROIS_INFERENCE = 1000
config = InferenceConfig()
config.display()
model_dir = os.path.join(caiman_datadir(), 'model')
DEVICE = "/cpu:0" # /cpu:0 or /gpu:0
with tf.device(DEVICE):
model = modellib.MaskRCNN(mode="inference",
model_dir=model_dir,
config=config)
weights_path = download_model('mask_rcnn')
model.load_weights(weights_path, by_name=True)
results = model.detect([summary_image], verbose=1)
r = results[0]
ROIs = r['masks'].transpose([2, 0, 1])
display_result = False
if display_result:
_, ax = plt.subplots(1, 1, figsize=(16, 16))
visualize.display_instances(summary_image,
r['rois'],
r['masks'],
r['class_ids'], ['BG', 'neurons'],
r['scores'],
ax=ax,
title="Predictions")
time_seg = time() - time_mmap - time_mc - time_start
print('Start SPIKE EXTRACTION')
# %% restart cluster to clean up memory
dview.terminate()
dview = Pool(n_processes, maxtasksperchild=1)
# %% parameters for trace denoising and spike extraction
fnames = fname_new # change file
ROIs = ROIs # region of interests
index = list(range(len(ROIs))) # index of neurons
weights = None # reuse spatial weights
tau_lp = 5 # parameter for high-pass filter to remove photobleaching
threshold = 4 # threshold for finding spikes, increase threshold to find less spikes
contextSize = 35 # number of pixels surrounding the ROI to censor from the background PCA
flip_signal = True # Important! Flip signal or not, True for Voltron indicator, False for others
opts_dict = {
'fnames': fnames,
'ROIs': ROIs,
'index': index,
'weights': weights,
'tau_lp': tau_lp,
'threshold': threshold,
'contextSize': contextSize,
'flip_signal': flip_signal
}
opts.change_params(params_dict=opts_dict)
#%% Trace Denoising and Spike Extraction
vpy = VOLPY(n_processes=n_processes, dview=dview, params=opts)
vpy.fit(n_processes=n_processes, dview=dview)
# %% STOP CLUSTER and clean up log files
#dview.terminate()
log_files = glob.glob('*_LOG_*')
for log_file in log_files:
os.remove(log_file)
time_ext = time() - time_mmap - time_mc - time_start - time_seg
#%%
print('file:' + fnames)
print('number of processes' + str(n_processes))
print(time_mc)
print(time_mmap)
print(time_seg)
print(time_ext)
time_list = [time_mc, time_mmap, time_seg, time_ext]
return time_list
def main():
pass # For compatibility between running under Spyder and the CLI
# %% Load demo movie and ROIs
fnames = download_demo('demo_voltage_imaging.hdf5', 'volpy') # file path to movie file (will download if not present)
path_ROIs = download_demo('demo_voltage_imaging_ROIs.hdf5', 'volpy') # file path to ROIs file (will download if not present)
# %% Setup some parameters for data and motion correction
# dataset parameters
fr = 400 # sample rate of the movie
ROIs = None # Region of interests
index = None # index of neurons
weights = None # reuse spatial weights by
# opts.change_params(params_dict={'weights':vpy.estimates['weights']})
# motion correction parameters
pw_rigid = False # flag for pw-rigid motion correction
gSig_filt = (3, 3) # size of filter, in general gSig (see below),
# change this one if algorithm does not work
max_shifts = (5, 5) # maximum allowed rigid shift
strides = (48, 48) # start a new patch for pw-rigid motion correction every x pixels
overlaps = (24, 24) # overlap between pathes (size of patch strides+overlaps)
max_deviation_rigid = 3 # maximum deviation allowed for patch with respect to rigid shifts
border_nan = 'copy'
opts_dict = {
'fnames': fnames,
'fr': fr,
'index': index,
'ROIs': ROIs,
'weights': weights,
'pw_rigid': pw_rigid,
'max_shifts': max_shifts,
'gSig_filt': gSig_filt,
'strides': strides,
'overlaps': overlaps,
'max_deviation_rigid': max_deviation_rigid,
'border_nan': border_nan
}
opts = volparams(params_dict=opts_dict)
# %% play the movie (optional)
# playing the movie using opencv. It requires loading the movie in memory.
# To close the video press q
display_images = False
if display_images:
m_orig = cm.load(fnames)
ds_ratio = 0.2
moviehandle = m_orig.resize(1, 1, ds_ratio)
moviehandle.play(q_max=99.5, fr=60, magnification=2)
# %% start a cluster for parallel processing
c, dview, n_processes = cm.cluster.setup_cluster(
backend='local', n_processes=None, single_thread=False)
# %%% MOTION CORRECTION
# Create a motion correction object with the specified parameters
mc = MotionCorrect(fnames, dview=dview, **opts.get_group('motion'))
# Run piecewise rigid motion correction
mc.motion_correct(save_movie=True)
dview.terminate()
# %% motion correction compared with original movie
display_images = False
if display_images:
m_orig = cm.load(fnames)
m_rig = cm.load(mc.mmap_file)
ds_ratio = 0.2
moviehandle = cm.concatenate([m_orig.resize(1, 1, ds_ratio) - mc.min_mov * mc.nonneg_movie,
m_rig.resize(1, 1, ds_ratio)], axis=2)
moviehandle.play(fr=60, q_max=99.5, magnification=2) # press q to exit
# % movie subtracted from the mean
m_orig2 = (m_orig - np.mean(m_orig, axis=0))
m_rig2 = (m_rig - np.mean(m_rig, axis=0))
moviehandle1 = cm.concatenate([m_orig2.resize(1, 1, ds_ratio),
m_rig2.resize(1, 1, ds_ratio)], axis=2)
moviehandle1.play(fr=60, q_max=99.5, magnification=2)
# %% Memory Mapping
c, dview, n_processes = cm.cluster.setup_cluster(
backend='local', n_processes=None, single_thread=False)
border_to_0 = 0 if mc.border_nan == 'copy' else mc.border_to_0
fname_new = cm.save_memmap_join(mc.mmap_file, base_name='memmap_',
add_to_mov=border_to_0, dview=dview, n_chunks=10)
dview.terminate()
# %% change fnames to the new motion corrected one
opts.change_params(params_dict={'fnames': fname_new})
# %% SEGMENTATION
# Create mean and correlation image
use_maskrcnn = True # set to True to predict the ROIs using the mask R-CNN
if not use_maskrcnn: # use manual annotations
with h5py.File(path_ROIs, 'r') as fl:
ROIs = fl['mov'][()] # load ROIs
opts.change_params(params_dict={'ROIs': ROIs,
'index': list(range(ROIs.shape[0])),
'method': 'SpikePursuit'})
else:
m = cm.load(mc.mmap_file[0], subindices=slice(0, 20000))
m.fr = fr
img = m.mean(axis=0)
img = (img-np.mean(img))/np.std(img)
m1 = m.computeDFF(secsWindow=1, in_place=True)[0]
m = m - m1
Cn = m.local_correlations(swap_dim=False, eight_neighbours=True)
img_corr = (Cn-np.mean(Cn))/np.std(Cn)
summary_image = np.stack([img, img, img_corr], axis=2).astype(np.float32)
del m
del m1
# %%
# Mask R-CNN
config = neurons.NeuronsConfig()
class InferenceConfig(config.__class__):
# Run detection on one image at a time
GPU_COUNT = 1
IMAGES_PER_GPU = 1
DETECTION_MIN_CONFIDENCE = 0.7
IMAGE_RESIZE_MODE = "pad64"
IMAGE_MAX_DIM = 512
RPN_NMS_THRESHOLD = 0.7
POST_NMS_ROIS_INFERENCE = 1000
config = InferenceConfig()
config.display()
model_dir = os.path.join(caiman_datadir(), 'model')
DEVICE = "/cpu:0" # /cpu:0 or /gpu:0
with tf.device(DEVICE):
model = modellib.MaskRCNN(mode="inference", model_dir=model_dir,
config=config)
weights_path = download_model('mask_rcnn')
model.load_weights(weights_path, by_name=True)
results = model.detect([summary_image], verbose=1)
r = results[0]
ROIs_mrcnn = r['masks'].transpose([2, 0, 1])
# %% visualize the result
display_result = False
if display_result:
_, ax = plt.subplots(1,1, figsize=(16,16))
visualize.display_instances(summary_image, r['rois'], r['masks'], r['class_ids'],
['BG', 'neurons'], r['scores'], ax=ax,
title="Predictions")
# %% set rois
opts.change_params(params_dict={'ROIs':ROIs_mrcnn,
'index':list(range(ROIs_mrcnn.shape[0])),
'method':'SpikePursuit'})
# %% Trace Denoising and Spike Extraction
c, dview, n_processes = cm.cluster.setup_cluster(
backend='local', n_processes=None, single_thread=False, maxtasksperchild=1)
vpy = VOLPY(n_processes=n_processes, dview=dview, params=opts)
vpy.fit(n_processes=n_processes, dview=dview)
# %% some visualization
print(np.where(vpy.estimates['passedLocalityTest'])[0]) # neurons that pass locality test
n = 0
# Processed signal and spikes of neurons
plt.figure()
plt.plot(vpy.estimates['trace'][n])
plt.plot(vpy.estimates['spikeTimes'][n],
np.max(vpy.estimates['trace'][n]) * np.ones(vpy.estimates['spikeTimes'][n].shape),
color='g', marker='o', fillstyle='none', linestyle='none')
plt.title('signal and spike times')
plt.show()
# Location of neurons by Mask R-CNN or manual annotation
plt.figure()
if use_maskrcnn:
plt.imshow(ROIs_mrcnn[n])
else:
plt.imshow(ROIs[n])
mv = cm.load(fname_new)
plt.imshow(mv.mean(axis=0),alpha=0.5)
# Spatial filter created by algorithm
plt.figure()
plt.imshow(vpy.estimates['spatialFilter'][n])
plt.colorbar()
plt.title('spatial filter')
plt.show()
# %% STOP CLUSTER and clean up log files
cm.stop_server(dview=dview)
log_files = glob.glob('*_LOG_*')
for log_file in log_files:
os.remove(log_file)
def run_caiman_pipeline(movie, fr, fnames, savedir, usematlabroi):
#%%
cpu_num = 7
cpu_num_spikepursuit = 2
#gsig_filt_micron = (4, 4)
#max_shifts_micron = (6,6)
#strides_micron = (60,60)
#overlaps_micron = (30, 30)
gsig_filt_micron = (4, 4)
max_shifts_micron = (6, 6)
strides_micron = (30, 30)
overlaps_micron = (15, 15)
max_deviation_rigid_micron = 4
pixel_size = movie['movie_pixel_size']
ROIs = None # Region of interests
index = None # index of neurons
weights = None # reuse spatial weights by
# opts.change_params(params_dict={'weights':vpy.estimates['weights']})
# motion correction parameters
pw_rigid = False # flag for pw-rigid motion correction
gSig_filt = tuple(
np.asarray(np.round(np.asarray(gsig_filt_micron) / float(pixel_size)),
int)) # size of filter, in general gSig (see below),
# change this one if algorithm does not work
max_shifts = tuple(
np.asarray(np.round(np.asarray(max_shifts_micron) / float(pixel_size)),
int))
strides = tuple(
np.asarray(np.round(np.asarray(strides_micron) / float(pixel_size)),
int)
) # start a new patch for pw-rigid motion correction every x pixels
overlaps = tuple(
np.asarray(np.round(np.asarray(overlaps_micron) / float(pixel_size)),
int)
) # start a new patch for pw-rigid motion correction every x pixels
# overlap between pathes (size of patch strides+overlaps)
max_deviation_rigid = int(
round(max_deviation_rigid_micron / pixel_size)
) # maximum deviation allowed for patch with respect to rigid shifts
border_nan = 'copy'
opts_dict = {
'fnames': fnames,
'fr': fr,
'index': index,
'ROIs': ROIs,
'weights': weights,
'pw_rigid': pw_rigid,
'max_shifts': max_shifts,
'gSig_filt': gSig_filt,
'strides': strides,
'overlaps': overlaps,
'max_deviation_rigid': max_deviation_rigid,
'border_nan': border_nan
}
opts = volparams(params_dict=opts_dict)
# %% play the movie (optional)
# playing the movie using opencv. It requires loading the movie in memory.
# To close the video press q
display_images = False
if display_images:
m_orig = cm.load(fnames)
ds_ratio = 0.2
moviehandle = m_orig.resize(1, 1, ds_ratio)
moviehandle.play(q_max=99.5, fr=60, magnification=2)
# %% start a cluster for parallel processing
c, dview, n_processes = cm.cluster.setup_cluster(backend='local',
n_processes=cpu_num,
single_thread=False)
# % MOTION CORRECTION
# Create a motion correction object with the specified parameters
mcrig = MotionCorrect(fnames, dview=dview, **opts.get_group('motion'))
# Run piecewise rigid motion correction
#%
mcrig.motion_correct(save_movie=True)
dview.terminate()
# % MOTION CORRECTION2
opts.change_params({'pw_rigid': True})
c, dview, n_processes = cm.cluster.setup_cluster(backend='local',
n_processes=cpu_num,
single_thread=False)
# Create a motion correction object with the specified parameters
mc = MotionCorrect(mcrig.mmap_file,
dview=dview,
**opts.get_group('motion'))
# Run piecewise rigid motion correction
mc.motion_correct(save_movie=True)
dview.terminate()
# %% motion correction compared with original movie
display_images = False
if display_images:
m_orig = cm.load(fnames)
m_rig = cm.load(mcrig.mmap_file)
m_pwrig = cm.load(mc.mmap_file)
ds_ratio = 0.2
moviehandle = cm.concatenate([
m_orig.resize(1, 1, ds_ratio) - mc.min_mov * mc.nonneg_movie,
m_rig.resize(1, 1, ds_ratio),
m_pwrig.resize(1, 1, ds_ratio)
],
axis=2)
moviehandle.play(fr=60, q_max=99.5, magnification=2) # press q to exit
# % movie subtracted from the mean
m_orig2 = (m_orig - np.mean(m_orig, axis=0))
m_rig2 = (m_rig - np.mean(m_rig, axis=0))
m_pwrig2 = (m_pwrig - np.mean(m_pwrig, axis=0))
moviehandle1 = cm.concatenate([
m_orig2.resize(1, 1, ds_ratio),
m_rig2.resize(1, 1, ds_ratio),
m_pwrig2.resize(1, 1, ds_ratio)
],
axis=2)
moviehandle1.play(fr=60, q_max=99.5, magnification=2)
# %% Memory Mapping
c, dview, n_processes = cm.cluster.setup_cluster(backend='local',
n_processes=cpu_num,
single_thread=False)
border_to_0 = 0 if mc.border_nan == 'copy' else mc.border_to_0
fname_new = cm.save_memmap_join(mc.mmap_file,
base_name='memmap_',
add_to_mov=border_to_0,
dview=dview,
n_chunks=10)
dview.terminate()
# %% change fnames to the new motion corrected one
opts.change_params(params_dict={'fnames': fname_new})
# %% SEGMENTATION
roidir = savedir[:savedir.find('VolPy')] + 'Spikepursuit' + savedir[
savedir.find('VolPy') + len('Volpy'):]
try:
files = os.listdir(roidir)
except:
files = []
if usematlabroi and 'ROIs.mat' in files:
ROIs = loadmat(os.path.join(roidir, 'ROIs.mat'))['ROIs']
if len(np.shape(ROIs)) == 3:
ROIs = np.moveaxis(np.asarray(ROIs, bool), 2, 0)
else:
ROIs = np.asarray([ROIs])
all_rois = ROIs
opts.change_params(
params_dict={
'ROIs': ROIs,
'index': list(range(ROIs.shape[0])),
'method': 'SpikePursuit'
})
else:
#%
print('WTF')
# Create mean and correlation image
use_maskrcnn = True # set to True to predict the ROIs using the mask R-CNN
if not use_maskrcnn: # use manual annotations
with h5py.File(path_ROIs, 'r') as fl:
ROIs = fl['mov'][()] # load ROIs
opts.change_params(
params_dict={
'ROIs': ROIs,
'index': list(range(ROIs.shape[0])),
'method': 'SpikePursuit'
})
else:
try:
m = cm.load(mc.mmap_file[0], subindices=slice(0, 20000))
except:
m = cm.load(
'/home/rozmar/Data/Voltage_imaging/Voltage_rig_1P/rozsam/20200120/40x_1xtube_10A_7_000_rig__d1_128_d2_512_d3_1_order_F_frames_2273_._els__d1_128_d2_512_d3_1_order_F_frames_2273_.mmap',
subindices=slice(0, 20000))
m.fr = fr
img = m.mean(axis=0)
img = (img - np.mean(img)) / np.std(img)
m1 = m.computeDFF(secsWindow=1, in_place=True)[0]
m = m - m1
Cn = m.local_correlations(swap_dim=False, eight_neighbours=True)
img_corr = (Cn - np.mean(Cn)) / np.std(Cn)
summary_image = np.stack([img, img, img_corr],
axis=2).astype(np.float32)
del m
del m1
# %
# Mask R-CNN
config = neurons.NeuronsConfig()
class InferenceConfig(config.__class__):
# Run detection on one image at a time
GPU_COUNT = 1
IMAGES_PER_GPU = 1
DETECTION_MIN_CONFIDENCE = 0.7
IMAGE_RESIZE_MODE = "pad64"
IMAGE_MAX_DIM = 512
RPN_NMS_THRESHOLD = 0.7
POST_NMS_ROIS_INFERENCE = 1000
config = InferenceConfig()
config.display()
model_dir = os.path.join(caiman_datadir(), 'model')
DEVICE = "/cpu:0" # /cpu:0 or /gpu:0
with tf.device(DEVICE):
model = modellib.MaskRCNN(mode="inference",
model_dir=model_dir,
config=config)
weights_path = download_model('mask_rcnn')
model.load_weights(weights_path, by_name=True)
results = model.detect([summary_image], verbose=1)
r = results[0]
ROIs_mrcnn = r['masks'].transpose([2, 0, 1])
# %% visualize the result
display_result = False
if display_result:
_, ax = plt.subplots(1, 1, figsize=(16, 16))
visualize.display_instances(summary_image,
r['rois'],
r['masks'],
r['class_ids'], ['BG', 'neurons'],
r['scores'],
ax=ax,
title="Predictions")
# %% set rois
opts.change_params(
params_dict={
'ROIs': ROIs_mrcnn,
'index': list(range(ROIs_mrcnn.shape[0])),
'method': 'SpikePursuit'
})
#all_rois = ROIs_mrcnn
# %% Trace Denoising and Spike Extraction
c, dview, n_processes = cm.cluster.setup_cluster(
backend='local',
n_processes=cpu_num_spikepursuit,
single_thread=False,
maxtasksperchild=1)
#dview=None
vpy = VOLPY(n_processes=n_processes, dview=dview, params=opts)
vpy.fit(n_processes=n_processes, dview=dview)
#%%
print('saving parameters')
parameters = dict()
parameters['motion'] = opts.motion
parameters['data'] = opts.data
parameters['volspike'] = opts.volspike
with open(os.path.join(savedir, 'parameters.pickle'), 'wb') as outfile:
pickle.dump(parameters, outfile)
#%%
volspikedata = dict()
volspikedata['estimates'] = vpy.estimates
volspikedata['params'] = vpy.params.data
with open(os.path.join(savedir, 'spikepursuit.pickle'), 'wb') as outfile:
pickle.dump(volspikedata, outfile)
#%%
for mcidx, mc_now in enumerate([mcrig, mc]):
motioncorr = dict()
motioncorr['fname'] = mc_now.fname
motioncorr['fname_tot_rig'] = mc_now.fname_tot_rig
motioncorr['mmap_file'] = mc_now.mmap_file
motioncorr['min_mov'] = mc_now.min_mov
motioncorr['shifts_rig'] = mc_now.shifts_rig
motioncorr['shifts_opencv'] = mc_now.shifts_opencv
motioncorr['niter_rig'] = mc_now.niter_rig
motioncorr['min_mov'] = mc_now.min_mov
motioncorr['templates_rig'] = mc_now.templates_rig
motioncorr['total_template_rig'] = mc_now.total_template_rig
try:
motioncorr['x_shifts_els'] = mc_now.x_shifts_els
motioncorr['y_shifts_els'] = mc_now.y_shifts_els
except:
pass
with open(
os.path.join(savedir, 'motion_corr_' + str(mcidx) + '.pickle'),
'wb') as outfile:
pickle.dump(motioncorr, outfile)
#%% saving stuff
print('moving files')
for mmap_file in mcrig.mmap_file:
fname = pathlib.Path(mmap_file).name
os.remove(mmap_file)
#shutil.move(mmap_file, os.path.join(savedir,fname))
for mmap_file in mc.mmap_file:
fname = pathlib.Path(mmap_file).name
os.remove(mmap_file)
#shutil.move(mmap_file, os.path.join(savedir,fname))
fname = pathlib.Path(fname_new).name
shutil.move(fname_new, os.path.join(savedir, fname))
#print('waiting')
#time.sleep(1000)
# %% some visualization
plotstuff = False
if plotstuff:
print(np.where(vpy.estimates['passedLocalityTest'])
[0]) # neurons that pass locality test
n = 0
# Processed signal and spikes of neurons
plt.figure()
plt.plot(vpy.estimates['trace'][n])
plt.plot(vpy.estimates['spikeTimes'][n],
np.max(vpy.estimates['trace'][n]) *
np.ones(vpy.estimates['spikeTimes'][n].shape),
color='g',
marker='o',
fillstyle='none',
linestyle='none')
plt.title('signal and spike times')
plt.show()
# Location of neurons by Mask R-CNN or manual annotation
plt.figure()
if use_maskrcnn:
plt.imshow(ROIs_mrcnn[n])
else:
plt.imshow(ROIs[n])
mv = cm.load(fname_new)
plt.imshow(mv.mean(axis=0), alpha=0.5)
# Spatial filter created by algorithm
plt.figure()
plt.imshow(vpy.estimates['spatialFilter'][n])
plt.colorbar()
plt.title('spatial filter')
plt.show()
# %% STOP CLUSTER and clean up log files
cm.stop_server(dview=dview)
log_files = glob.glob('*_LOG_*')
for log_file in log_files:
os.remove(log_file)