Sami's Developpement #4
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Corrections
Modified Display and Style.
Modified Display of Patch size in the Config Frame.
Modified inputs of patch size , augmentation patch size and number of pool . Added function to preprocess, autoconfig, save config, print path to config, and update text boxes after run. Modified button colors and size .
Added remote train and autoconfig.
Added new argument (Remote) to use when on Remote.
Added popup messages. Redefined dropdown menus.
Added some popup messages. Added test to create required folders.
Added Parameters return function.
…o 2D_Segmentation
src/biom3d/auto_config.py
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| ) | ||
| parameters_return(patch, pool, batch, config_path) | ||
| except: | ||
| print("[Error] Import error. Biom3d must be installed if you want to save your configuration. Another solution is to config the function function in biom3d.utils here...") |
GuillaumeMougeot
requested changes
May 14, 2024
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| if args.remote: | ||
| try: | ||
| from biom3d.utils import save_python_config |
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duplica avec lignes 401 à 411. peut être essayer de compresser
| @@ -279,15 +291,23 @@ def get_aug_patch(patch_size): | |||
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| # ---------------------------------------------------------------------------- | |||
| # Display | |||
| def parameters_return(patch, pool, batch, config_path): | |||
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a quoi sert cette fonction? documentation
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indiquer le type de sortie
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indiquer le type de sortie
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indiquer le type de sortie
src/biom3d/preprocess.py
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| @@ -417,7 +434,10 @@ def __init__( | |||
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| self.num_channels = 1 | |||
| self.channel_axis = 0 | |||
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| # Make sur the Channel dim is first ( we assume that the channel dim is the smallest dimension ! ) | |||
src/biom3d/preprocess.py
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| @@ -662,6 +685,7 @@ def auto_config_preprocess( | |||
| print("Standard deviation of intensities:", std) | |||
| print("0.5% percentile of intensities:", perc_005) | |||
| print("99.5% percentile of intensities:", perc_995) | |||
| print(" Image Type : ",is2d) | |||
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retirer l'espace avant Image
src/biom3d/preprocess.py
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| @@ -788,6 +817,8 @@ def auto_config_preprocess( | |||
| help="(default=False) Whether to print auto-config parameters. Used for remote preprocessing using the GUI.") | |||
| parser.add_argument("--debug", default=False, action='store_true', dest='debug', | |||
| help="(default=False) Debug mode. Whether to print all image filenames while preprocessing.") | |||
| parser.add_argument("--is2d", default=False, | |||
| help="(default=False) Check wheter the image has 2d only.") | |||
src/biom3d/upload_pred.py
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biom3d a déjà un ficher qui se nomme omero_uploader, l'utiliser plutot que celui ci-dessous
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Je ne l'utilise plus, c'est un ancien module que j'avais oublié de supprimer
| @@ -309,7 +308,8 @@ def tif_read_imagej(img_path, axes_order='CZYX'): | |||
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| img = tiff.tifffile.transpose_axes(img, series.axes, axes_order) | |||
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| img_meta["axes"] = axes_order | |||
| #img_meta["axes"] = axes_order | |||
| img_meta["axes"] = series.axes | |||
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ça marche ça ? c'était ça le bug des dimensions?
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Oui, c'était pour le bug des Z et T inversés
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