Merge pull request #3 from zoccoler/rev1

Rev1

Author: zoccoler

README.md

@@ -13,7 +13,50 @@ Clone this repository locally (for example using [Github Desktop](https://deskto
 From a command line prompt, navigate to where you cloned this repository locally (for example by typing `cd Lifetime-Separation`) and create a specific conda environment by typing the following line:
 
 ```bash
-mamba env create -f env.yml
+mamba env create -f env_pinned.yml
+```
+
+## Data
+
+The input raw data used by this repository can be found in the [BioImage Archive](https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD1967).
+
+The code only needs local access to the `.zarr` and `.xml` files. Download these and place them in a folder structure like this (preferably inside the `Lifetime-Separation` local repository):
+
+```
+Lifetime-Separation
+|
+├─ embryos_data
+|    |
+|    ├─ LP307_1_sptw
+|    |    |
+|    |    ├─ LP307_1_sptw.zarr
+|    |    └─ LP307_1.xml
+|    |    
+|    |
+|    ├─ LP307_2_sptw
+|    |    |
+|    |    ├─ LP307_2_sptw.zarr
+|    |    └─ LP307_2.xml
+|    ⁞ 
+|    # rest of the embryos data
+|
+├─ worms_data
+|    |
+|    ├─ AZ212_sptw
+|    |    |
+|    |    ├─ AZ212_sptw.zarr
+|    |    └─ AZ212.xml
+|    |    
+|    |
+|    └─ JJ1473_sptw
+|         |
+|         ├─ JJ1473_sptw.zarr
+|         └─ JJ1473.xml
+|  
+├─ code  
+|    |     
+⁞     ⁞
+# rest of the repository code
 ```
 
 ## Usage

code/phasor_plot_AZ212.ipynb

@@ -9,7 +9,7 @@
 
 from napari_flim_phasor_plotter.filters import apply_binning
 from napari_flim_phasor_plotter._reader import read_stack
-from napari_flim_phasor_plotter._widget import make_flim_phasor_plot, manual_label_extract, smooth_cluster_mask
+from napari_flim_phasor_plotter.widgets import make_flim_phasor_plot, manual_label_extract, smooth_cluster_mask
 
 from utilities import ellipse_vertices, format_metadata, set_plot_zoom_position, add_segmentation_metadata
 import time
@@ -23,9 +23,9 @@
 # Inputs
 
 # Main folder path (each folder contains a zarr file and an xml file)
-main_folder_path = Path("/home/pol_haase/mazo260d/Data/I227_Lifetime_Unmixing_of_Dyes_with_Overlapping_Sprectra/Batch_Processing")
+main_folder_path = Path("../embryos_data/")
 
-# Additional metadata in case the xml file is not available
+# Additional manual metadata if xml file was not available (not the case)
 z_pixel_size = 0.5*1e-6 # in m
 pixel_size_unit = 'm'
 time_resolution_per_slice = 0.663 # in seconds
@@ -282,7 +282,7 @@
         # Convert the segmentation result to a Dask array
         chunk_shape = summed_intensity_stack.chunksize
         cluster_labels_image_timelapse_dask = da.from_array(cluster_labels_image_timelapse_post_processed, chunks=chunk_shape)
-        
+    
         if store_phasor_mask:
             cluster_mask_timelapse = np.expand_dims(cluster_mask_timelapse.astype(summed_intensity_stack.dtype), axis=0)
             cluster_mask_timelapse_dask = da.from_array(cluster_mask_timelapse, chunks=chunk_shape)
@@ -307,6 +307,14 @@
         # Writing to the file
         with open(file_path, 'w') as file:
             file.write(f"sample_name = {sample_name}\n")
+            file.write(f"data shape = {data.shape}\n")
+            file.write(f"laser_frequency = {laser_frequency} MHz\n")
+            file.write(f"x_pixel_size = {metadata_timelapse['PhysicalSizeX']} {metadata_timelapse['PhysicalSizeXUnit']}\n")
+            file.write(f"y_pixel_size = {metadata_timelapse['PhysicalSizeY']} {metadata_timelapse['PhysicalSizeYUnit']}\n")
+            file.write(f"z_pixel_size = {metadata_timelapse['PhysicalSizeZ']} {metadata_timelapse['PhysicalSizeZUnit']}\n")
+            file.write(f"time_resolution = {metadata_timelapse['TimeIncrement']} {metadata_timelapse['TimeIncrementUnit']}\n")
+            file.write(f"microtime_resolution = {metadata_single_timepoint['TimeIncrement']} {metadata_single_timepoint['TimeIncrementUnit']}\n")
+            file.write(f"channel_names = {channel_names}\n")
             file.write(f"center = {center}\n")
             file.write(f"major-axis = {major}\n")
             file.write(f"minor-axis = {minor}\n")