tlambert03

<?xml version="1.0" encoding="utf-8" ?>
<!-- transformation for clipboard actions (cut copy paste) -->
<!-- layout specific -->
<layouts>
    <!-- Dvorak X C V are not on same physical position as on US keyboard. -->
    <layout name="com.apple.keylayout.Dvorak">
        <transformations>
            <!-- Command+X to Control+X -->
            <transform>
                <from command="1" key="B" />

tlambert03

import os
import dask.array as da
from dask import delayed
from skimage.io import imread
from skimage.external import tifffile as tf
from glob import glob
import re

delayed_read = delayed(imread)

tlambert03

getting started with napari

This describes how to get started with napari in a full python environment, from scratch.

Install anaconda or miniconda

There are many ways to get python on your computer. You can just go to https://www.python.org/downloads/ to get python, but anaconda is nice for two reasons:

1. It provides a built in "environment" manager (called conda) that allows you to create isolated virtual environments (which are basically just folders somewhere on your computer that have, among other things, a handful of packages that you have installed). Virtual environments are useful because you can easily create multiple environments with different combinations of packages and versions without messing up your "root" environment (more on this below).
2. For some combinations of packages, it can be hard to get them all working together, so Anaconda ships with a complete working environment that already contains [the main packages in the scientific python stack](https://docs.anaconda.com/an

tlambert03

"""
example of using napari to show model predictions as they update.
requires stuff from https://github.com/jni/noise2self
"""
import torch
from torch.utils.data import DataLoader, Dataset
from torchvision import datasets, transforms

import napari
from mask import Masker

tlambert03

#!/bin/zsh

## RUN WITH:
# curl https://bit.ly/33mby8d -o bootstrap
# chmod +x bootstrap
# ./bootstrap

###############################################################################
# Install Xcode command line tools
###############################################################################

tlambert03

STYLES = {
    "double": {
        "TOP": ("╔", "╤", "╗", "═"),
        "MID": ("╟", "┼", "╢", "─"),
        "BOT": ("╚", "╧", "╝", "═"),
        "V": ("║", "│"),
    },
    "heavy": {
        "TOP": ("┏", "┯", "┓", "━"),
        "MID": ("┠", "┼", "┨", "─"),

tlambert03

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
~/miniconda3/envs/napdev/lib/python3.9/site-packages/magicgui/widgets/_bases/value_widget.py in (*x=(False,))
     42         self.changed = EventEmitter(source=self, type="changed")
     43         self._widget._mgui_bind_change_callback(
---> 44             lambda *x: self.changed(value=x[0] if x else None)
        x = (False,)
        global self.changed = undefined
        global value = undefined

tlambert03

from dataclasses import dataclass
from typing import Optional, Type

import napari
import inspect
from napari.utils.events import EventedModel
from napari.utils.settings._defaults import BaseNapariSettings
from napari.components.viewer_model import ViewerModel

tlambert03

import os
import sys
import time
from pathlib import Path

SAFE_WORD = "delete"  # if this word is in the filename, it won't be deleted


def find_userd(noinput=False):
    # detect user directory

tlambert03

from typing import Generic, TypeVar, Any, Literal, Union, overload
import numpy as np

DType = TypeVar("DType")
Shape = TypeVar("Shape")

class Array(Generic[Shape, DType]): ...

# a way to temporarily discuss shapes,
# until we can use PEP 646