Merge branch 'master' into som_memory

README.md

@@ -94,7 +94,13 @@ First, get the latest version of the code
 git pull
 ```
 
-Then, run the command below to update the jupyter notebooks to the latest version
+Check for Docker updates by running:
+
+```
+docker pull angelolab/ark-analysis:latest
+```
+
+Then, run the command below to update the Jupyter notebooks to the latest version
 ```
 ./start_docker.sh --update
 ```
@@ -103,8 +109,6 @@ or
 ./start_docker.sh -u
 ```
 
-If the requirements.txt has changed, Docker will rebuild with the new dependencies first.
-
 ### WARNING
 
 If you didn't change the name of any of the notebooks within the `scripts` folder, they will be overwritten by the command above! 

ark/utils/load_utils.py

@@ -6,7 +6,7 @@
 import xarray as xr
 
 from ark.utils.tiff_utils import read_mibitiff
-from ark.utils import io_utils as iou
+from ark.utils import io_utils as iou, misc_utils
 
 
 def load_imgs_from_mibitiff(data_dir, mibitiff_files=None, channels=None, delimiter=None,
@@ -96,8 +96,9 @@ def load_imgs_from_tree(data_dir, img_sub_folder=None, fovs=None, channels=None,
             directory containing folders of images
         img_sub_folder (str):
             optional name of image sub-folder within each fov
-        fovs (list):
-            optional list of folders to load imgs from. Default loads all folders
+        fovs (str, list):
+            optional list of folders to load imgs from, or the name of a single folder. Default
+            loads all folders
         channels (list):
             optional list of imgs to load, otherwise loads all imgs
         dtype (str/type):
@@ -121,6 +122,10 @@ def load_imgs_from_tree(data_dir, img_sub_folder=None, fovs=None, channels=None,
     if len(fovs) == 0:
         raise ValueError(f"No fovs found in directory, {data_dir}")
 
+    # If the fov provided is a single string (`fov_1` instead of [`fov_1`])
+    if type(fovs) is str:
+        fovs = [fovs]
+
     if img_sub_folder is None:
         # no img_sub_folder, change to empty string to read directly from base folder
         img_sub_folder = ""
@@ -147,6 +152,11 @@ def load_imgs_from_tree(data_dir, img_sub_folder=None, fovs=None, channels=None,
         # get the corresponding indices found in channels_no_delim
         channels_indices = [channels_no_delim.index(chan.split('.')[0]) for chan in all_channels]
 
+        # verify if channels from user input are present in `all_channels`
+        all_channels_no_delim = [channel.split('.')[0] for channel in all_channels]
+
+        misc_utils.verify_same_elements(all_channels_in_folder=all_channels_no_delim,
+                                        all_channels_detected=channels_no_delim)
         # reorder back to original
         channels = [chan for _, chan in sorted(zip(channels_indices, all_channels))]
 

ark/utils/load_utils_test.py

@@ -137,6 +137,19 @@ def test_load_imgs_from_tree():
 
         assert loaded_xr.equals(data_xr)
 
+        # check when fov is a single string
+        loaded_xr = \
+            load_utils.load_imgs_from_tree(temp_dir, img_sub_folder="TIFs", dtype="int16",
+                                           fovs='fov0', channels=some_chans)
+
+        assert loaded_xr.equals(data_xr[:1, :, :, :2])
+
+        # check that an error raises when a channel provided does not exist
+        with pytest.raises(ValueError):
+            loaded_xr = \
+                load_utils.load_imgs_from_tree(temp_dir, img_sub_folder="TIFs", dtype="int16",
+                                               channels=['chan4'])
+
     # test loading with data_xr containing float values
     with tempfile.TemporaryDirectory() as temp_dir:
         fovs, chans, imgs = test_utils.gen_fov_chan_names(num_fovs=1, num_chans=2,

docs/_rtd/windows_setup.md

@@ -48,6 +48,23 @@ To run the script, you have to use `bash start_docker.sh`. If you run into issue
 * Run `wsl sudo apt-get install dos2unix`
 * Run `wsl dos2unix start_docker.sh` and `wsl dos2unix update_notebooks.sh`
 
+
+### Mounting External Drives
+
+If you wish to mount an external drive to the Docker instance you may do so by adding an argument to the execution of the `start_docker.sh` script.
+
+If, for example the data is stored on `X:/path/to/external/data/` where `X:/` is your external drive name, you will need to add:
+
+```bash
+bash start_docker.sh --external "/mnt/x/path/to/external/data"
+```
+
+`X:/` has to be swapped with `/mnt/x/` to be a valid path on WSL. In addition `--external` has a shorthand notation: `-e`.
+```bash
+bash start_docker.sh -e "/mnt/x/path/to/external/data"
+```
+
+
 ### If you run into more Windows-specific issues
 
 Please open an [issue](https://github.com/angelolab/ark-analysis/issues) on our GitHub page. Note that our codebase has not been extensively tested on Windows.

start_docker.sh

@@ -33,6 +33,13 @@ done
 # find lowest open port available
 PORT=8888
 
+if [ $update -ne 0 ]
+  then
+    bash update_notebooks.sh -u
+  else
+    bash update_notebooks.sh
+fi
+
 until [[ $(docker container ls | grep 0.0.0.0:$PORT | wc -l) -eq 0 ]]
   do
     ((PORT=$PORT+1))