diff --git a/openflexure_microscope/api/app.py b/openflexure_microscope/api/app.py index ad12c6b5..52ca01ab 100644 --- a/openflexure_microscope/api/app.py +++ b/openflexure_microscope/api/app.py @@ -1,10 +1,6 @@ #!/usr/bin/env python from gevent import monkey - -# Patch most system modules. Leave threads untouched so we can still use them normally if needed. -print("Monkey patching with Gevenet") monkey.patch_all() -print("Monkey patching successful") import time import atexit diff --git a/openflexure_microscope/api/default_extensions/scan.py b/openflexure_microscope/api/default_extensions/scan.py index a5f82f52..ef788a05 100644 --- a/openflexure_microscope/api/default_extensions/scan.py +++ b/openflexure_microscope/api/default_extensions/scan.py @@ -198,6 +198,7 @@ def tile( else: # Run slow autofocus. Client should provide dz ~ 50 autofocus_extension.autofocus( + microscope, range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz) ) logging.debug("Finished autofocus") diff --git a/poetry.lock b/poetry.lock index 9dd6737c..5fdf5085 100644 --- a/poetry.lock +++ b/poetry.lock @@ -277,7 +277,7 @@ description = "Python implementation of LabThings, based on the Flask microframe name = "labthings" optional = false python-versions = ">=3.6,<4.0" -version = "0.3.0" +version = "0.4.0" [package.dependencies] Flask = ">=1.1.1,<2.0.0" @@ -358,12 +358,13 @@ version = "1.13.2b0" [package.extras] array = ["numpy"] doc = ["sphinx"] -test = ["coverage", "pytest", "mock", "pillow", "numpy"] +test = ["pillow", "coverage", "mock", "numpy", "pytest"] [package.source] reference = "79177fa7f28d6d5c6eab5ba814b420b1785b6b24" type = "git" url = "https://github.com/rwb27/picamera.git" + [[package]] category = "main" description = "Python Imaging Library (Fork)" @@ -716,7 +717,7 @@ ifaddr = "*" rpi = ["picamera", "RPi.GPIO"] [metadata] -content-hash = "71b15705721aa7447357d24e79c6ff77f6844b4191eceb5e90a14942c5375b91" +content-hash = "f7bb806f267f9f38aedfe6bb4ef6d23deef9df991c7117bd58f8c0e83c64b2b4" python-versions = "^3.6" [metadata.files] @@ -883,8 +884,8 @@ jinja2 = [ {file = "Jinja2-2.11.1.tar.gz", hash = "sha256:93187ffbc7808079673ef52771baa950426fd664d3aad1d0fa3e95644360e250"}, ] labthings = [ - {file = "labthings-0.3.0-py3-none-any.whl", hash = "sha256:605999a8fe09a52ad32a4763020b81e5d1b7b786478b47e1f45594aa10bcdd2d"}, - {file = "labthings-0.3.0.tar.gz", hash = "sha256:cc93ee4510fc1304a450346e11d0069541142e8867cfcf8e4381a872abf16a6c"}, + {file = "labthings-0.4.0-py3-none-any.whl", hash = "sha256:75fe8f65b89783bb852ad4d1463b2f721ea42f03ae06fbe3df76b85d8c65eac1"}, + {file = "labthings-0.4.0.tar.gz", hash = "sha256:e6b5c6c322915808f8833ec9aa81c7ede08282a0946a28562b5ca77549099ef4"}, ] lazy-object-proxy = [ {file = "lazy-object-proxy-1.4.3.tar.gz", hash = "sha256:f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0"}, @@ -937,6 +938,11 @@ markupsafe = [ {file = "MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:ba59edeaa2fc6114428f1637ffff42da1e311e29382d81b339c1817d37ec93c6"}, {file = "MarkupSafe-1.1.1-cp37-cp37m-win32.whl", hash = "sha256:b00c1de48212e4cc9603895652c5c410df699856a2853135b3967591e4beebc2"}, {file = "MarkupSafe-1.1.1-cp37-cp37m-win_amd64.whl", hash = "sha256:9bf40443012702a1d2070043cb6291650a0841ece432556f784f004937f0f32c"}, + {file = "MarkupSafe-1.1.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:6788b695d50a51edb699cb55e35487e430fa21f1ed838122d722e0ff0ac5ba15"}, + {file = "MarkupSafe-1.1.1-cp38-cp38-manylinux1_i686.whl", hash = "sha256:cdb132fc825c38e1aeec2c8aa9338310d29d337bebbd7baa06889d09a60a1fa2"}, + {file = "MarkupSafe-1.1.1-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:13d3144e1e340870b25e7b10b98d779608c02016d5184cfb9927a9f10c689f42"}, + {file = "MarkupSafe-1.1.1-cp38-cp38-win32.whl", hash = "sha256:596510de112c685489095da617b5bcbbac7dd6384aeebeda4df6025d0256a81b"}, + {file = "MarkupSafe-1.1.1-cp38-cp38-win_amd64.whl", hash = "sha256:e8313f01ba26fbbe36c7be1966a7b7424942f670f38e666995b88d012765b9be"}, {file = "MarkupSafe-1.1.1.tar.gz", hash = "sha256:29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b"}, ] marshmallow = [ diff --git a/pyproject.toml b/pyproject.toml index 37a4659c..c9f02312 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,7 +35,7 @@ pyserial = "^3.4" # Used for sangaboard (basic_serial_instrument) until we move python-dateutil = "^2.8" psutil = "^5.6.7" # Autostorage extension -labthings = "0.3.0" +labthings = "0.4.0" [tool.poetry.extras] rpi = ["picamera", "RPi.GPIO"]