Merge pull request #17 from neutrons/from_sample_to_peak_suffix

substitute "sample" with "peak"

.github/pull_request_template.md

@@ -7,7 +7,6 @@ Check all that apply:
 - [ ] Source added/refactored
 - [ ] Added unit tests
 - [ ] Added integration tests
-- [ ] Verified that tests requiring the /SNS and /HFIR filesystems pass without fail
 
 **References:**
 - Links to IBM EWM items:
@@ -25,19 +24,3 @@ updated, or an explanation is provided as to why release notes are unnecessary
 - [ ] All the tests are passing
 - [ ] The documentation is up to date
 - [ ] code comments added when explaining intent
-
-### Execution of tests requiring the /SNS and /HFIR filesystems
-It is strongly encouraged that the reviewer runs the following tests in their local machine
-because these tests are not run by the GitLab CI. It is assumed that the reviewer has the /SNS and /HFIR filesystems
-remotely mounted in their machine.
-
-```bash
-cd /path/to/my/local/mr_reduction/repo/
-git fetch origin merge-requests/<MERGE_REQUEST_NUMBER>/head:mr<MERGE_REQUEST_NUMBER>
-git switch mr<MERGE_REQUEST_NUMBER>
-conda activate <my_mr_reduction_environment>
-pytest -m mount_eqsans ./tests/unit/ ./tests/integration/
-```
-In the above code snippet, substitute `<MERGE_REQUEST_NUMBER>` for the actual merge request number. Also substitute
-`<my_mr_reduction_environment>` with the name of the conda environment you use for development. It is critical that
-you have installed the repo in editable mode with `pip install -e .` or `conda develop .`

docs/index.rst

@@ -10,7 +10,7 @@ User Guide
 .. toctree::
    :titlesonly:
 
-   /user/multiple_samples
+   /user/multiple_peaks
    /user/conda_environments
    /user/reduce
    /releases

docs/releases.rst

@@ -10,7 +10,7 @@ Notes for major and minor releases. Notes for patch releases are referred.
 
 **Of interest to the User**:
 
-- PR #9 Add the capability to autoreduce two samples from the same run
+- PR #9 Add the capability to autoreduce two peaks from the same run
 
 **Of interest to the Developer:**
 

docs/user/multiple_peaks.rst

@@ -0,0 +1,22 @@
+.. multiple_peaks
+
+Multiple Peaks in a single Run
+================================
+
+The Magnetism Reflectometer can stack several (usually 2, rarely 3) peaks on top of each other.
+The beam is wide enough to cover all the peaks.
+To measure reflectivity, the beam is very narrow in the other direction (so it’s like a thin ribbon).
+Because we are sensitive to tiny angles,
+the reflection from each peak will appear in different sports on the detector.
+With one peak, there will be one spot on the detector.
+With two, there will be two if (1) the peaks are not exactly parallel
+(in which case it will still look like one spot) and
+(2) the peaks are parallel enough so that both spots are on the detector
+(otherwise one of the spots may be outside the detector surface.
+
+.. figure:: ./media/two_peaks_stacked.png
+   :alt: Reflectometry from two peaks stacked.
+   :align: center
+   :width: 900
+
+   Reflectometry from two peaks stacked.

docs/user/reduce.rst

@@ -49,27 +49,27 @@ Notice how the report shows the superposition of reflectivity curves for runs 41
 will happen if reduced files for runs 41446 and 41447 are found either in the output directory `/tmp/test_webform`
 or the canonical output directory for autoreduction of runs corresponding to run 41445 which in this
 case is `/SNS/REF_M/IPTS-21391/shared/autoreduce/`. Runs 41445, 41446, and 41447 correspond to experiments
-taken on the same sample but with a different incidence angle.
+taken on the same peak but with a different incidence angle.
 
-The webapp supports reduction of up to three samples for the scenarios when the run contains more than one sample.
-In the following screenshot we selected `Sample Count=2`, causing reduction taking into account options
-from `Sample #1` and `Sample #2`.
+The webapp supports reduction of up to three peaks for the scenarios when the run contains more than one peak.
+In the following screenshot we selected `Peak Count=2`, causing reduction taking into account options
+from `Peak #1` and `Peak #2`.
 
-.. figure:: ./media/manual_reduction_two_samples.GIF
-   :alt: Reduction of two samples.
+.. figure:: ./media/manual_reduction_two_peaks.GIF
+   :alt: Reduction of two peaks.
    :align: center
    :width: 900
 
-   Reduction of two samples.
+   Reduction of two peaks.
 
-The below excerpt from the corresponding report show the reflectivity curves for the two samples (41445_1 and 41445_2).
+The below excerpt from the corresponding report show the reflectivity curves for the two peaks (41445_1 and 41445_2).
 
-.. figure:: ./media/manual_reduction_two_samples_report.GIF
-   :alt: Report for two samples.
+.. figure:: ./media/manual_reduction_two_peaks_report.GIF
+   :alt: Report for two peaks.
    :align: center
    :width: 700
 
-   Report for two samples.
+   Report for two peaks.
 
 
 Automated Reduction

src/mr_autoreduce/reduce_REF_M.py.template

@@ -45,7 +45,7 @@ def _as_bool(value):
 
 def reduction_user_options():
     r"""Collects all values defined by the user in https://monitor.sns.gov/reduction/ref_m/"""
-    # Options common to all samples:
+    # Options common to all peaks:
     kwargs_common = dict(
         plot_2d=_as_bool(${plot_in_2D}),
         const_q_binning=_as_bool(${use_const_q}),
@@ -55,8 +55,8 @@ def reduction_user_options():
         publish = False  # uploading to livedata server to be done later by `upload_html_report()`
     )
 
-    # Options for Sample 1
-    kwargs_sample_1 = dict(
+    # Options for Peak 1
+    kwargs_peak_1 = dict(
         use_roi=True,
         force_peak_roi=_as_bool(${force_peak}),
         peak_roi=[int(${peak_min}), int(${peak_max})],
@@ -67,8 +67,8 @@ def reduction_user_options():
         bck_offset=int(${bck_width})
     )
 
-    # Options for Sample 2
-    kwargs_sample_2 = dict(
+    # Options for Peak 2
+    kwargs_peak_2 = dict(
         use_roi=True,
         force_peak_roi=_as_bool(${force_peak_s2}),
         peak_roi=[int(${peak_min_s2}), int(${peak_max_s2})],
@@ -79,8 +79,8 @@ def reduction_user_options():
         bck_offset=int(${bck_width_s2})
     )
 
-    # Options for Sample 3
-    kwargs_sample_3 = dict(
+    # Options for Peak 3
+    kwargs_peak_3 = dict(
         use_roi=True,
         force_peak_roi=_as_bool(${force_peak_s3}),
         peak_roi=[int(${peak_min_s3}), int(${peak_max_s3})],
@@ -91,22 +91,22 @@ def reduction_user_options():
         bck_offset=int(${bck_width_s3}),
     )
 
-    # Do we have more than one sample in this run?
-    sample_count = int(${sample_count})
-    ReductionOptions = namedtuple('ReductionOptions', 'common, sample_count, sample1, sample2, sample3')
-    return ReductionOptions(kwargs_common, sample_count, kwargs_sample_1, kwargs_sample_2, kwargs_sample_3)
+    # Do we have more than one peak in this run?
+    peak_count = int(${peak_count})
+    ReductionOptions = namedtuple('ReductionOptions', 'common, peak_count, peak1, peak2, peak3')
+    return ReductionOptions(kwargs_common, peak_count, kwargs_peak_1, kwargs_peak_2, kwargs_peak_3)
 
 
 def reduce_events_file(event_file_path, outdir):
     event_file = os.path.split(event_file_path)[-1]  # file name
-    reports = list()  # autoreduction reports for each sample in the run, in HTML format
+    reports = list()  # autoreduction reports for each peak in the run, in HTML format
     opts = reduction_user_options()
-    assert opts.sample_count <= 3, "Sample count must be <= 3"
-    kwargs_samples = [opts.sample1, opts.sample2, opts.sample3]
-    sample_numbers = [None, ] if opts.sample_count == 1 else range(1, opts.sample_count + 1)  # numbers start at 1, not 0
-    for i, sample_number in enumerate(sample_numbers):
-        d = dict(data_run=event_file, output_dir=outdir, sample_number=sample_number)
-        kwargs = {**d, **opts.common, **kwargs_samples[i]}  # merge all partial dicts
+    assert opts.peak_count <= 3, "Peak count must be <= 3"
+    kwargs_peaks = [opts.peak1, opts.peak2, opts.peak3]
+    peak_numbers = [None, ] if opts.peak_count == 1 else range(1, opts.peak_count + 1)  # numbers start at 1, not 0
+    for i, peak_number in enumerate(peak_numbers):
+        d = dict(data_run=event_file, output_dir=outdir, peak_number=peak_number)
+        kwargs = {**d, **opts.common, **kwargs_peaks[i]}  # merge all partial dicts
         reports.append(ReductionProcess(**kwargs).reduce())
     return reports
 

src/mr_autoreduce/templates/reduction_options.html

@@ -26,11 +26,11 @@
             padding: 5px;
             margin-bottom: 10px;
         }
-        .samples-container {
+        .peaks-container {
             display: flex;
             justify-content: space-between;
         }
-        .sample {
+        .peak {
             width: 30%;
             padding: 10px;
             box-sizing: border-box;
@@ -53,7 +53,7 @@ <h2 title="Output directory path for reduced and reports files">Output Directory
         </div>
 
         <div class="form-section">
-            <h2>Options for all samples</h2>
+            <h2>Options for all peaks</h2>
 
             <label title="Check the following box to see 2D plots on the monitor.
 Loading the page for each run will take much longer when this option is turned on.">
@@ -66,19 +66,19 @@ <h2>Options for all samples</h2>
             <label title="Check the following box if you want to use SANGLE,
 otherwise DANGLE will be used."><input type="checkbox" id="use_sangle" checked> Use SANGLE</label>
 
-            <label title="Once the reflected peak ROI is selected for each sample below,
+            <label title="Once the reflected peak ROI is selected for each peak below,
 you can try to fine tune this ROI by fitting for a peak within that
 region and updating the ROI [both center and width] according to the
 location found. Check the box if you want to find a peak within the
 ROI and redefine the ROI afterwards."><input type="checkbox" id="fit_peak_in_roi" checked> Automated ROI</label>
 
-            <label title="Number of samples in the run" style="font-weight:bold; font-size:1.2em;">
-                Sample count <input type="number" id="sample_count" style="width: 25px;" value="1"></label>
+            <label title="Number of peaks in the run" style="font-weight:bold; font-size:1.2em;">
+                Peak count <input type="number" id="peak_count" style="width: 25px;" value="1"></label>
         </div>
 
-        <div class="samples-container">
-            <div class="form-section sample" id="sample1">
-                <h2>Sample #1</h2>
+        <div class="peaks-container">
+            <div class="form-section peak" id="peak1">
+                <h2>Peak #1</h2>
 
                 <label title="You can choose to replace the ROI in the data by your own range.
 Check the following box if you want to define your own ROI and
@@ -109,8 +109,8 @@ <h2>Sample #1</h2>
                 <label>Pixels on each side <input type="number" style="width: 40px;" id="bck_width"></label>
             </div>
 
-            <div class="form-section sample" id="sample2">
-                <h2 title="Sample 2 options ignored if Sample count is 1">Sample #2</h2>
+            <div class="form-section peak" id="peak2">
+                <h2 title="Peak 2 options ignored if Peak count is 1">Peak #2</h2>
 
                 <label title="You can choose to replace the ROI in the data by your own range.
 Check the following box if you want to define your own ROI and
@@ -141,8 +141,8 @@ <h2 title="Sample 2 options ignored if Sample count is 1">Sample #2</h2>
                 <label>Pixels on each side <input type="number" style="width: 40px;" id="bck_width_s2"></label>
             </div>
 
-            <div class="form-section sample" id="sample3">
-                <h2 title="Sample 3 options ignored if Sample count is smaller than three">Sample #3</h2>
+            <div class="form-section peak" id="peak3">
+                <h2 title="Peak 3 options ignored if Peak count is smaller than three">Peak #3</h2>
 
                 <label title="You can choose to replace the ROI in the data by your own range.
 Check the following box if you want to define your own ROI and
@@ -228,7 +228,7 @@ <h2 title="Sample 3 options ignored if Sample count is smaller than three">Sampl
                 q_step: document.getElementById('q_step').value,
                 use_sangle: document.getElementById('use_sangle').checked,
                 fit_peak_in_roi: document.getElementById('fit_peak_in_roi').checked,
-                sample_count: document.getElementById('sample_count').value,
+                peak_count: document.getElementById('peak_count').value,
 
                 force_peak: document.getElementById('force_peak').checked,
                 peak_min: document.getElementById('peak_min').value,