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bug-fix/NaN error in examples #178

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bug-fix/NaN error in examples #178

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4669a36
Fix NaN error running example
zsdqui Oct 19, 2020
c8e445a
Add prediction dirs to gitignore
zsdqui Nov 9, 2020
d4754c3
Remove extra "/" in paths
zsdqui Nov 9, 2020
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5 changes: 5 additions & 0 deletions .gitignore
View file
Original file line number Diff line number Diff line change
@@ -25,6 +25,11 @@ wheels/
.installed.cfg
*.egg

# Data/Predictions
fovs*
model*
predictions*

# OS generated files
.DS_Store

8 changes: 3 additions & 5 deletions examples/download_and_train.py
View file
Original file line number Diff line number Diff line change
@@ -34,7 +34,7 @@
n_images_to_download = args.n_imgs # more images the better
train_fraction = 0.75

image_save_dir = "{}/".format(os.getcwd())
image_save_dir = "{}".format(os.getcwd())
model_save_dir = "{}/model/".format(os.getcwd())
prefs_save_path = "{}/prefs.json".format(model_save_dir)

@@ -82,10 +82,8 @@
df = pd.DataFrame(columns=["path_tiff", "channel_signal", "channel_target"])

df["path_tiff"] = image_target_paths
df["channel_signal"] = data_manifest["ChannelNumberBrightfield"]
df["channel_target"] = data_manifest[
"ChannelNumber405"
] # this is the DNA channel for all FOVs
df["channel_signal"] = data_manifest["ChannelNumberBrightfield"].tolist()
df["channel_target"] = data_manifest["ChannelNumber405"].tolist() # this is the DNA channel for all FOVs

n_train_images = int(n_images_to_download * train_fraction)
df_train = df[:n_train_images]