Elizabeth/try local install

README.md

@@ -8,9 +8,8 @@ This project is divided into three main parts: the Pylon camera interface, the N
 
 You'll need to install some Python and Node packages to run these three components.
 
-1. Create the `bloom-desktop` environment: `mamba create --name bloom-desktop`
+1. Create the `bloom-desktop` environment with python 3.8 and nodejs: `mamba create --name bloom-desktop python=3.8 nodejs=18 pip -c conda-forge`
 2. Activate the environment: `mamba activate bloom-desktop`
-3. Install conda requirements: `mamba install python=3.8 nodejs nidaqmx`
 3. Install pip requirements:
    `pip install -r requirements.txt`
 

app/README.md

@@ -2,17 +2,27 @@
 
 ## Installation
 
-1. Create `./.env` in this directory (see `.env.example`).
-2. Edit `./.env` with an appropriate database file location.
-3. Create `$HOME/.bloom/desktop-config.yaml` (see `desktop-config.yaml.example`).
-4. Edit `$HOME/.bloom/desktop-config.yaml` with the correct database file location and other values.
-5. Run `npm install`.
-6. Run `npm run client:generate` to generate Typescript client for the new schema.
-7. Run `npm run db:deploy` to create the database.
+1. `mamba activate bloom-desktop`
+2. Follow the instructions in (bloom)[https://gitlab.com/salk-tm/bloom/-/tree/main?ref_type=heads] to setup a local supabase instance to interact with, and add some test data.
+3. Create `./.env` in this directory (see `.env.example`).
+4. Edit `./.env` with an appropriate database file location.
+5. Create `$HOME/.bloom/desktop-config.yaml` (see `desktop-config.yaml.example`).
+    - References test images located at `test\sample_scan`.
+    - Use the same environment variables as in https://gitlab.com/salk-tm/bloom/-/blob/main/web/env.dev to configure bloom-desktop to work with your local supabase instance.
+6. Edit `$HOME/.bloom/desktop-config.yaml` with the correct database file location and other values.
+7. Run `npm install`.
+    - Make sure you are in `app` directory. 
+    - Build tools required for this step:
+         - https://visualstudio.microsoft.com/ C++ for Desktop Development on Windows
+         - XCode for Mac
+         - `build-essential` for Linux
+    - Use `npm cache clean` to cleanup
+8. Run `npm run client:generate` to generate Typescript client for the new schema (`app\prisma\schema.prisma`)
+9. Run `npm run db:deploy` to create the database and apply the migrations.
 
 ## Quickstart
 
-Run `npm run start`.
+Run `npm run start` from `app` directory.
 
 ## Modifying the database
 

pylon/pylon_fake.py

@@ -6,10 +6,15 @@
 import sys
 import time
 import pathlib
+import logging
 
 import imageio.v2 as iio
 
-sample_scan = '/Users/djbutler/dev/bloom-desktop-pilot/test/sample_scan'
+logging.basicConfig(level=logging.INFO)
+
+# Test images are in "test/sample_scan" directory from the root of the repo
+sample_scan = pathlib.Path(__file__).parent.parent / "test" / "sample_scan"
+logging.info(f"sample_scan: {sample_scan}")
 
 
 async def save_image_async(executor, output_path, idx, array):

pylon/pylon_stream_forever_fake.py

@@ -6,6 +6,7 @@
 import sys
 import time
 import pathlib
+import logging
 
 import base64
 from io import BytesIO
@@ -14,12 +15,18 @@
 
 import imageio.v2 as iio
 
-sample_scan = "/Users/djbutler/dev/bloom-desktop-pilot/test/sample_scan"
+logging.basicConfig(level=logging.INFO)
+
+# Test images are in "test/sample_scan" directory from the root of the repo
+sample_scan = pathlib.Path(__file__).parent.parent / "test" / "sample_scan"
+logging.info(f"sample_scan: {sample_scan}")
+
 
 
 def stream_frames(camera_settings):
     n = camera_settings["num_frames"]
     src_frames = glob.glob(os.path.join(sample_scan, "*.png"))
+    logging.debug(f"Found {len(src_frames)} frames.")
     src_frames.sort(key=lambda x: int(os.path.basename(x).split(".")[0]))
     i = 0
     while True:
@@ -29,6 +36,7 @@ def stream_frames(camera_settings):
         # time the function call
         start = time.time()
         img = iio.imread(src_frame)
+        logging.debug(f"Read {src_frame}.")
         end = time.time()
         # print(f"iio.imread took {end - start} seconds", file=sys.stderr)
         # time the function call
@@ -41,11 +49,17 @@ def stream_frames(camera_settings):
 
 
 def img_to_base64(img):
-    buffer = BytesIO()
-    pil_img = Image.fromarray(img)
-    pil_img.save(buffer, format="PNG", compress_level=0)
-    # iio.imwrite(buffer, img, ".png")
-    base64_img = base64.b64encode(buffer.getvalue()).decode("utf-8")
+    if img is None or img.size == 0:
+        logging.error("Invalid image encountered!")
+        return ""
+
+    with BytesIO() as buffer:
+        with Image.fromarray(img) as pil_img:
+            logging.debug(f"{pil_img} opened.")
+            pil_img.save(buffer, format="PNG", compress_level=0)
+            logging.debug(f"{pil_img} saved to buffer.")
+        base64_img = base64.b64encode(buffer.getvalue()).decode("utf-8")
+        logging.debug(f"base64_img: {base64_img[:100]}")
     return base64_img