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microscope object that can scan in xyzt #27

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85b56e6
Merge pull request #25 from ndsystems/development
pskeshu Mar 31, 2021
edc4cf3
made object detection algorithm 3D
pskeshu Apr 16, 2021
345a116
defined a special case of imshow
pskeshu Apr 16, 2021
8420412
simulated microscope now sends a noisy stage timelapse
pskeshu Apr 16, 2021
ced76df
cleaned up run by defining a Microscope, with higher level bluesky ca…
pskeshu Apr 16, 2021
56ff8f6
access pandas dataframe
pskeshu Apr 16, 2021
d631849
isort-ed import statements
pskeshu Apr 16, 2021
436a2a7
replace for loop with list comprehension
pskeshu Apr 16, 2021
4e3b385
comments
pskeshu Apr 19, 2021
c8bcd6a
return label only
pskeshu Apr 19, 2021
4a6a8ed
stage init
pskeshu Apr 19, 2021
116727f
added comments
pskeshu Apr 19, 2021
b43fce4
more user code
pskeshu Apr 19, 2021
4127ccc
added label layer
pskeshu Apr 19, 2021
4b86d38
added support for xystage in ophyd
pskeshu May 3, 2021
5040a5e
Stage as a pseudopositioner
pskeshu May 3, 2021
774a078
#D02-3 livetiffexport of images for manual access
pskeshu May 7, 2021
f4447c8
working xy scan code
pskeshu May 10, 2021
e02f4ab
channel config
pskeshu May 11, 2021
8d186b7
cleaned up run
pskeshu May 11, 2021
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21 changes: 21 additions & 0 deletions deepthought/comms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,19 @@
import rpyc
from rpyc.utils.server import ThreadedServer


def server(object_, port, *args, **kwargs):
"""serving an object in a port.

parameters
--
object_ : object
any python object that needs to be network enabled.
port : int
defines the port where the server is listening for requests.


"""
s = ThreadedServer(object_, hostname="", port=port, auto_register=None,
protocol_config={"allow_all_attrs": True,
"allow_pickle" : True,
Expand All @@ -12,6 +24,15 @@ def server(object_, port, *args, **kwargs):
return s

def client(addr, port, *args, **kwargs):
"""generic function to connect to a rpyc server.

parameters
--
addr : str
ip address/url of the server
port : int
port
"""
obj = rpyc.connect(addr, port, config={
"allow_all_attrs": True, "allow_pickle" : True
})
Expand Down
21 changes: 15 additions & 6 deletions deepthought/configs.py
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Original file line number Diff line number Diff line change
@@ -1,26 +1,35 @@
from collections import OrderedDict
from collections import OrderedDict
import os

config = OrderedDict()


def abspath(path):
return os.path.abspath(path)


def read_env_value(name, default):
if name in os.environ:
value = os.environ[name]
else:
value = default
return value


MM_DIR = {
"name" : "MM_DIR",
"default" : "C:\Program Files\Micro-Manager-2.0gamma"
"name": "MM_DIR",
"default": "C:\Program Files\Micro-Manager-2.0gamma"
}
MM_CONFIG = {
"name" : "MM_CONFIG",
"default" : "./mmconfigs/Bright_Star.cfg"
"name": "MM_CONFIG",
"default": "./mmconfigs/Bright_Star.cfg"
}
MM_SERVER = {
"name": "MM_SERVER",
"default": "localhost",
}

config["mm_dir"] = abspath(read_env_value(**MM_DIR))
config["mm_config"] = abspath(read_env_value(**MM_CONFIG))
config["mm_server"] = {"addr": read_env_value(**MM_SERVER), "port": 18861}
store_disk = True
# feature toggle
8 changes: 7 additions & 1 deletion deepthought/detection.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
import numpy as np
import tifffile
from cellpose import models

Expand Down Expand Up @@ -27,5 +28,10 @@ def detect_object(image, kind="dapi"):
elif kind == "cyto":
seg_func = segment_cyto

if image.shape[0] > 1:
labels_ = np.array([seg_func(img) for img in image])

return labels_

label_ = seg_func(image)
return (image, label_)
return label_
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