Tests etc (#179)

* Add multiposition test to TIFF test

* Move config files out of GitHub repo

src/aslm/config/__init__.py

@@ -0,0 +1 @@
+from .config import *

src/aslm/config/config.py

@@ -0,0 +1,40 @@
+import os
+import shutil
+import platform
+from pathlib import Path
+
+def get_configuration_paths():
+    # Establish a base directory in AppData/.ASLM for Windows or ~/.ASLM for Mac and Linux
+    if platform.system() == 'Windows':
+        base_directory = os.getenv('APPDATA')
+    else:
+        base_directory = os.getenv('HOME')
+    aslm_directory = os.path.join(base_directory, '.ASLM')
+    if not os.path.exists(aslm_directory):
+        os.mkdir(aslm_directory)
+    configuration_directory = Path(os.path.join(aslm_directory, 'config'))
+    if not os.path.exists(configuration_directory):
+        os.mkdir(configuration_directory)
+
+    # Configuration files should be stored in this directory
+    configuration_path = Path.joinpath(configuration_directory, 'configuration.yml')
+    experiment_path = Path.joinpath(configuration_directory, 'experiment.yml')
+    etl_constants_path = Path.joinpath(configuration_directory, 'etl_constants.yml')
+
+    # If they are not already, copy the default ones that ship with the software too this folder
+    if not os.path.exists(configuration_path):
+        copy_base_directory = Path(__file__).resolve().parent
+        copy_configuration_path = Path.joinpath(copy_base_directory, 'configuration.yml')
+        shutil.copyfile(copy_configuration_path, configuration_path)
+
+    if not os.path.exists(experiment_path):
+        copy_base_directory = Path(__file__).resolve().parent
+        copy_experiment_path = Path.joinpath(copy_base_directory, 'experiment.yml')
+        shutil.copyfile(copy_experiment_path, experiment_path)
+
+    if not os.path.exists(etl_constants_path):
+        copy_base_directory = Path(__file__).resolve().parent
+        copy_etl_constants_path = Path.joinpath(copy_base_directory, 'etl_constants.yml')
+        shutil.copyfile(copy_etl_constants_path, etl_constants_path)
+
+    return configuration_path, experiment_path, etl_constants_path

src/aslm/main.py

@@ -36,6 +36,7 @@
 import tkinter as tk
 import platform
 from aslm.log_files.log_functions import log_setup
+from aslm.config import get_configuration_paths
 
 # Local Imports
 from aslm.controller.aslm_controller import ASLM_controller as Controller
@@ -64,14 +65,8 @@ def main():
     python main.py --synthetic_hardware
     """
 
-    # Specify the Default Configuration File Directories (located in src/config)
-    base_directory = Path(__file__).resolve().parent
-    configuration_directory = Path.joinpath(base_directory, 'config')
-
-    # Full file paths.
-    configuration_path = Path.joinpath(configuration_directory, 'configuration.yml')
-    experiment_path = Path.joinpath(configuration_directory, 'experiment.yml')
-    etl_constants_path = Path.joinpath(configuration_directory, 'etl_constants.yml')
+    # Specify the Default Configuration paths
+    configuration_path, experiment_path, etl_constants_path = get_configuration_paths()
 
     # Parse command line arguments
     parser = argparse.ArgumentParser(description='Multiscale Microscope Command Line Arguments')

test/model/model_features/data_sources/test_tiff_data_source.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-def tiff_write_read(is_ome=False):
+def tiff_write_read(is_ome=False, multiposition=False):
     from aslm.model.dummy_model import get_dummy_model
     from aslm.model.model_features.data_sources.tiff_data_source import TiffDataSource
 
@@ -11,6 +11,8 @@ def tiff_write_read(is_ome=False):
     z_steps = np.random.randint(1,10)
     model.experiment.MicroscopeState['image_mode'] = 'z-stack'
     model.experiment.MicroscopeState['number_z_steps'] = z_steps
+    if multiposition:
+        model.experiment.MicroscopeState['is_multiposition'] = True
 
     # Establish a TIFF data source
     if is_ome:
@@ -20,16 +22,19 @@ def tiff_write_read(is_ome=False):
     ds = TiffDataSource(fn)
     ds.set_metadata_from_configuration_experiment(model.configuration, model.experiment)
 
-    # Populate one image per channel per timepoint
-    n_images = ds.shape_c*ds.shape_z*ds.shape_t
+    # Populate one image per channel per timepoint per positioj
+    n_images = ds.shape_c*ds.shape_z*ds.shape_t*ds.positions
     data = np.random.rand(n_images, ds.shape_x, ds.shape_y)
+    file_names = []
     for i in range(n_images):
         ds.write(data[i,...].squeeze())
+        c, z, _, _ = ds._cztp_indices(i, True)
+        if c == 0 and z == 0:
+            file_names.extend(ds.file_name)
     ds.close()
 
     # For each file...
-    for i, fn in enumerate(ds.file_name):
-        print(fn)
+    for i, fn in enumerate(file_names):
         ds2 = TiffDataSource(fn, 'r')
         # Make sure XYZ size is correct (and C and T are each of size 1)
         assert((ds2.shape_x == ds.shape_x) and (ds2.shape_y == ds.shape_y) \
@@ -41,16 +46,21 @@ def tiff_write_read(is_ome=False):
 
     try:
         # Clean up
-        for fn in ds.file_name:
+        dirs = []
+        for fn in file_names:
             os.remove(fn)
+            dirs.append(os.path.dirname(fn))
+        for dn in list(set(dirs)):
+            os.rmdir(dn)
     except PermissionError:
         # Windows seems to think these files are still open
         pass
 
-
 def test_tiff_write_read():
     tiff_write_read(False)
 
-
 def test_tiff_write_read_ome():
     tiff_write_read(True)
+
+def test_tiff_write_read_ome_multiposition():
+    tiff_write_read(True, True)