From a474399985064f7aa29ab5be9c8c2a5f2fa29a54 Mon Sep 17 00:00:00 2001
From: Carlos Sevilla Salcedo <carlossevillasalcedo@gmail.com>
Date: Fri, 8 Dec 2023 17:11:00 +0100
Subject: [PATCH] Adapt RGB to template

---
 .../DataProcessing/DataProcessing_core.py     |  2 +-
 .../DataProcessing/plugins/RGBprocessing.py   | 21 ++++++++++--
 .../materialdesign_processing_demo.xml        | 32 +++++++++++++++++--
 3 files changed, 50 insertions(+), 5 deletions(-)

diff --git a/src/vai_lab/DataProcessing/DataProcessing_core.py b/src/vai_lab/DataProcessing/DataProcessing_core.py
index 19d2c576..a963b44c 100644
--- a/src/vai_lab/DataProcessing/DataProcessing_core.py
+++ b/src/vai_lab/DataProcessing/DataProcessing_core.py
@@ -37,7 +37,7 @@ def launch(self) -> None:
                 out = getattr(self._plugin, "{}".format(method))()
 
         self.output_data = self._data_in.copy()
-        if len(out) > 0 and (isinstance(out[0], DataFrame) or isinstance(out[0], array)):
+        if len(self._module_config["plugin"]["methods"]["_order"]) > 0 and len(out) > 0 and (isinstance(out[0], DataFrame) or isinstance(out[0], array)):
             self.output_data.data[list(out[1])[0]] = out[0]
 
     def get_result(self) -> DataInterface:
diff --git a/src/vai_lab/DataProcessing/plugins/RGBprocessing.py b/src/vai_lab/DataProcessing/plugins/RGBprocessing.py
index 46d0fac3..23471e13 100644
--- a/src/vai_lab/DataProcessing/plugins/RGBprocessing.py
+++ b/src/vai_lab/DataProcessing/plugins/RGBprocessing.py
@@ -11,6 +11,7 @@
 from scipy.integrate import simps
 import numpy as np
 from vai_lab._plugin_templates import DataProcessingT
+from vai_lab._import_helper import rel_to_abs
 
 _PLUGIN_READABLE_NAMES = {"RGBprocessing": "default",
                           "rgbprocessing": "alias",}          # type:ignore
@@ -64,7 +65,23 @@ def __init__(self, folder, compositions, cutoff = None, is_calibrated = True, is
         else:
             filenames = ['sample_Ll.csv', 'sample_La.csv', 'sample_Lb.csv']
         
-        os.chdir(folder)
+        if type(compositions) is str:
+            if os.path.isabs(compositions):
+                try:
+                    compositions = pd.read_csv(compositions).get("Sample")
+                except Exception as exc:
+                    print('The plugin encountered an error trying to read the provided path to compositions: \"'
+                            +compositions+'\"')
+                    raise
+            else:
+                try:
+                    compositions = pd.read_csv(rel_to_abs(compositions)).get("Sample")
+                except Exception as exc:
+                    print('The plugin encountered an error trying to read the provided path to compositions: \"'
+                            +compositions+'\"')
+                    raise
+
+        os.chdir(rel_to_abs(folder))
         self.compositions = compositions
         compositions = pd.Series(compositions)
         
@@ -89,7 +106,7 @@ def __init__(self, folder, compositions, cutoff = None, is_calibrated = True, is
             self.green = self.green.iloc[:self.time.shape[0],:]
     
     def preprocess(self, normalize = None):
-        time_col = pd.DataFrame(pd.np.tile(self.time.values, (self.red.shape[1], 1)))
+        time_col = pd.DataFrame(np.tile(self.time.values, (self.red.shape[1], 1)))
         red = self.red.melt(var_name='columns')
         green = self.green.melt(var_name='columns')
         blue = self.blue.melt(var_name='columns')
diff --git a/src/vai_lab/examples/xml_files/materialdesign_processing_demo.xml b/src/vai_lab/examples/xml_files/materialdesign_processing_demo.xml
index fc4c5ea9..98324e48 100644
--- a/src/vai_lab/examples/xml_files/materialdesign_processing_demo.xml
+++ b/src/vai_lab/examples/xml_files/materialdesign_processing_demo.xml
@@ -8,7 +8,6 @@
         </coordinates>
     </Initialiser>
     <DataProcessing name="Data Processing">
-        <plugin type="" />
         <inputdata>
             <X module="Initialiser" />
         </inputdata>
@@ -19,9 +18,28 @@
         <coordinates>
             [(350.0, 350.0), 2, {0: 'd0-u2'}]
         </coordinates>
+        <plugin type="RGBprocessing">
+            <options>
+                <folder>
+                     .\examples\crystalDesign\20190606-R1-JT\BMP\RGB\Calibrated
+                </folder>
+                <compositions>
+                     .\examples\crystalDesign\20190606-R1-JT\BMP\RGB\Calibrated\Samples.csv
+                </compositions>
+            </options>
+            <method type="fit">
+                <options />
+            </method>
+            <method type="transform">
+                <options>
+                    <method>
+                         area
+                    </method>
+                </options>
+            </method>
+        </plugin>
     </DataProcessing>
     <Output name="Output">
-        <plugin type="" />
         <inputdata>
             <X module="Data Processing" />
         </inputdata>
@@ -31,5 +49,15 @@
         <coordinates>
             [(350.0, 650), 1, {2: 'd2-u1'}]
         </coordinates>
+        <plugin type="Output">
+            <options>
+                <outdata>
+                    Data Processing
+                </outdata>
+                <outpath>
+                     .\examples\results\output.pkl
+                </outpath>
+            </options>
+        </plugin>
     </Output>
 </pipeline>